Identification and characterization of miR-92a and its targets modulating Vibrio splendidus challenged Apostichopus japonicus

Vibrio splendidus infection promotes circRNA-FGL1-regulated coelomocyte apoptosis via competitive binding to Myc with the deubiquitinase OTUB1 in Apostichopus japonicus

Circular RNAs (circRNAs) are involved in various physiological and pathological processes in both vertebrates and invertebrates. However, most studies on circRNAs have focused on their roles as endogenous competitive RNAs. Here, we report a novel function of circRNA derived from the Fibrinogen-like protein 1 gene (circ-FGL1) that inhibits coelomocyte apoptosis via competing with the deubiquitinase AjOTUB1 to bind AjMyc in Apostichopus japonicus during Vibrio splendidus infection. The results showed that circ-FGL1 is significantly downregulated in coelomocytes of V. splendidus-induced A. japonicus and negatively regulates coelomocyte apoptosis through the AjBax-AjCyt c pathway. Mechanistically, the deubiquitinase AjOTUB1 and circ-FGL1 could interact with the transcription factor protein AjMyc in the same region with circ-FGL1/AjMyc having greater affinity. Under normal conditions, high levels of circ-FGL1 bind directly to AjMyc, inhibiting the deubiquitylation of AjMyc by AjOTUB1 and leading to the degradation of AjMyc. After V. splendidus infection, AjMyc disassociates from the depressed expression of circ-FGL1, promoting its deubiquitylation by binding to the induced deubiquitinase AjOTUB1 to inhibit its degradation. AjMyc is then transferred to nucleus and promotes the transcription of AjCyt c and AjBax to induce coelomocyte apoptosis. The new finding will expand our present outstanding on the functional role of circRNAs and suggests new therapeutic targets for the treatment of echinoderms during bacterial invasion.

Characterization of c-Jun N-terminal kinase (JNK) gene reveals involvement of immune defense against Vibrio splendidus infection in Apostichopus japonicus

The c-Jun N-terminal kinase (JNK) constitutes an evolutionarily conserved family of serine/threonine protein kinases, pivotal in regulating various physiological processes in vertebrates, encompassing apoptosis and antibacterial immunity. Nevertheless, the involvement of JNK in the innate immune response remains largely unexplored in pathogen-induced echinoderms. We isolated and characterized the JNK gene from Apostichopus japonicus (AjJNK) in our investigation. The full-length cDNA sequences of AjJNK spanned 1806 bp, comprising a 1299 bp open reading frame (ORF) encoding 432 amino acids, a 274 bp 5'-untranslated region (UTR), and a 233 bp 3'-UTR. Structural analysis revealed the presence of a classical S_TKc domain (37-335 amino acids) within AjJNK and contains several putative immune-related transcription factor-binding sites, including Elk-1, NF-κB, AP-1, and STAT5. Spatial expression analysis indicated ubiquitous expression of AjJNK across all examined tissues, with the highest expression noted in coelomocytes. The mRNA, protein, and phosphorylation levels of AjJNK were obviously induced in coelomocytes upon V. splendidus challenge and lipopolysaccharide stimulation. Immunofluorescence analysis demonstrated predominant cytoplasmic localization of AjJNK in coelomocytes with subsequent nuclear translocation following the V. splendidus challenge in vivo. Moreover, siRNA-mediated knockdown of AjJNK led to a significant increase in intracellular bacterial load, as well as elevated levels of Ajcaspase 3 and coelomocyte apoptosis post V. splendidus infection. Furthermore, the phosphorylation levels of AjJNK inhibited by its specific inhibitor SP600125 and also significantly suppressed the expression of Ajcaspase 3 and coelomocyte apoptosis during pathogen infection. Collectively, these data underscored the pivotal role of AjJNK in immune defense, specifically in the regulation of coelomocyte apoptosis in V. splendidus-challenged A. japonicus.

Akirin2 enhances antibacterial ability via interacting with 14-3-3ζ in V. splendidus-challenged Apostichopus japonicus

Akirin2 is pivotal for regulating host immunological responses in vertebrates, including antibacterial immunity and inflammation. However, the functional significance of Akirin2 in invertebrates remains largely unexplored. In this study, we cloned the complete cDNA sequence of Akirin2 from A. japonicus (AjAkirin2) and elucidated its immunological mechanism upon pathogen infection. The whole AjAkirin2 cDNA sequence spanned 1014 bp, which comprised a 630 bp open reading frame encoding 209 amino acids, a 230 bp 5'-untranslated region (UTR), and a 154 bp 3'-UTR. Spatial expression analysis displayed constitutive expression of AjAkirin2 in all examined tissues. Both mRNA and protein expression abundance of the AjAkirin2 showed considerably high in coelomocytes of sea cucumbers challenged with Vibrio splendidus or stimulated with lipopolysaccharide. In addition, we found that sea cucumbers with 107 CFU/mL V. splendidus infection had a lower survival rate upon AjAkirin2 knockdown. Mechanistically, the result of GST-pull down and co-IP assays indicated that AjAkirin2 directly interacted with Aj14-3-3ζ. Moreover, we also detected that AjAkirin2 positively regulated Aj14-3-3ζ expression in sea cucumber coelomocytes. Furthermore, the knockdown of AjAkirin2 or Aj14-3-3ζ resulted in increasing intracellular bacteria load and suppressed the expression of key genes of the NF-κB signaling pathway (p65 and p105) and inflammatory cytokines including IL-17, VEGF, and MMP-1. In summary, these results confirmed the critical role of AjAkirin2 in mediating innate immune responses against V. splendidus infection via interaction with Aj14-3-3ζ and thereby exerting antibacterial function.

NEDD4 activates mitophagy by interacting with LC3 to restrain reactive oxygen species and apoptosis in Apostichopus japonicus challenged with Vibrio splendidus

Mitophagy, the selective degradation of damaged mitochondria by autophagy, plays a crucial role in the survival of coelomocytes in Apostichopus japonicus following Vibrio splendidus infection by suppressing the generation of reactive oxygen species (ROS) and attenuating cell apoptosis. A recent study revealed that reducing the expression of the neural precursor cell-expressed developmentally downregulated gene 4 (NEDD4), an enzyme 3 (E3) ubiquitin ligase, significantly affects mitochondrial degradation. Prior to the present study, the functional role of NEDD4 in marine invertebrates was largely unexplored. Therefore, we investigated the role of NEDD4 in the activation of mitophagy, modulation of ROS levels, and induction of apoptosis in A. japonicus infected with V. splendidus. The results demonstrated that V. splendidus infection and lipopolysaccharide (LPS) challenge significantly increased the mRNA levels of NEDD4 in A. japonicus coelomocytes, which was consistent with changes in mitophagy under the same conditions. Knockdown of AjNEDD4 using specific small interfering RNAs (siRNAs) impaired mitophagy and caused accumulation of damaged mitochondria, as observed using transmission electron microscopy (TEM) and confocal microscopy. Furthermore, AjNEDD4 was localized to the mitochondria in both coelomocytes and HEK293T cells. Simultaneously, coelomocytes were treated with the inhibitor indole-3-carbinol (I3C) to confirm the regulatory role of AjNEDD4 in mitophagy. The accumulation of AjNEDD4 in the mitochondria and the level of mitophagy decreased. Subsequent investigations demonstrated that AjNEDD4 interacts directly with the microtubule-associated protein light chain 3 (LC3), a key regulator of autophagy and mitophagy, indicating its involvement in the mitophagy pathway. Moreover, AjNEDD4 interference hindered the interaction between AjNEDD4 and LC3, thereby impairing the engulfment and subsequent clearance of damaged mitochondria. Finally, AjNEDD4 interference led to a significant increase in intracellular ROS levels, followed by increased apoptosis. Collectively, these findings suggest that NEDD4 acts as a crucial regulator of mitophagy in A. japonicus and plays a vital role in maintaining cellular homeostasis following V. splendidus infection. NEDD4 suppresses ROS production and subsequent apoptosis by promoting mitophagy, thereby safeguarding the survival of A. japonicus under pathogenic conditions. Further investigation of the mechanisms underlying NEDD4-mediated mitophagy may provide valuable insights into the development of novel strategies for disease control in aquaculture farms.

ATGL-mediated lipophagy balances cholesterol-induced inflammation in pathogen infected Apostichopus japonicus coelomocytes

Cholesterol metabolism can be dynamically altered in response to pathogen infection that ensure proper macrophage inflammatory function in mammals. However, it is unclear whether the dynamic between cholesterol accumulation and breakdown could induce or suppress inflammation in aquatic animal. Here, we aimed to investigate the cholesterol metabolic response to LPS stimulation in coelomocytes of Apostichopus japonicus, and to elucidate the mechanism of lipophagy in regulating cholesterol-related inflammation. LPS stimulation significantly increased intracellular cholesterol levels at early time point (12 h), and the increase in cholesterol levels is associated with AjIL-17 upregulation. Excessive cholesterol in coelomocytes of A. japonicus was rapidly converted to cholesteryl esters (CEs) and stored in lipid droplets (LDs) after 12 h of LPS stimulation and prolonged for 18 h. Then, increased colocalization of LDs with lysosomes was observed at late time point of LPS treatment (24 h), accompanied by elevated expression of AjLC3 and decreased expression of Ajp62. At the same time, the expression of AjABCA1 rapidly increased, suggesting lipophagy induction. Moreover, we demonstrated that AjATGL is required for induction of lipophagy. Inducing lipophagy by AjATGL overexpression attenuated cholesterol-induced AjIL-17 expression. Overall, our study provides evidence that cholesterol metabolic response occurs upon LPS stimulation, which is actively involved in regulating the inflammatory response of coelomocytes. AjATGL-mediated lipophagy is responsible for cholesterol hydrolysis, thereby balancing cholesterol-induced inflammation in the coelomocytes of A. japonicus.

PPARα alleviates inflammation via inhibiting NF-κB/Rel pathway in Vibrio splendidus challenged Apostichopus japonicus

Organisms trigger pro-inflammatory responses to resist the invasion of foreign pathogens in the early infection stage. However, excessive or chronic inflammation can also cause several diseases. We previously validated IL-17 from sea cucumbers mediated inflammatory response by the IL-17R-TRAF6 axis. But the anti-inflammatory effect was largely unknown in the species. In this study, the conserved PPARα gene was obtained from Apostichopus japonicus by RNA-seq and RACE approaches. The expression of AjPPARα was found to be significantly induced at the late stage of infection not only in Vibrio splendidus-challenged sea cucumbers, but also in LPS-exposed coelomocytes, which was negative correlation to that of AjIL-17 and AjNLRP3. Both silencing AjPPARα by specific siRNA and treatment with AjPAPRα inhibitor MK-886 could significantly upregulate the transcriptional levels of pro-inflammatory factors the AjIL-17 and AjNLRP3. The infiltration of inflammatory cells and tissues damage were also detected in the body walls in the same condition. In contrast, AjPAPRα agonist of WY14643 treatment could alleviate the V. splendidus-induced tissue injury. To further explore the molecular mechanism of AjPPARα-mediated anti-inflammatory in A. japonicus, the expression of the transcriptional factors of AjStat5 and AjRel (subunit of NF-κB) were investigated under AjPPARα aberrant expression conditions and found that AjRel exhibited a negative regulatory relationship to AjPPARα. Furthermore, silencing AjRel was led to down-regulation of AjIL-17 and AjNLRP3. Taken together, our results supported that AjPPARα exerted anti-inflammatory effects through inhibiting AjRel in response to V. splendidus infection.

circRNA432 enhances the coelomocyte phagocytosis via regulating the miR-2008-ELMO1 axis in Vibrio splendidus-challenged Apostichopus japonicus

Circular RNAs (circRNAs) are a kind of extensive and diverse covalently closed circular endogenous RNA, which exert crucial functions in immune regulation in mammals. However, the functions and mechanisms of circRNAs in invertebrates are largely unclarified. In our previous work, 261 differentially expressed circRNAs including circRNA432 (circ432) were identified from skin ulcer syndrome (SUS) diseased sea cucumber Apostichopus japonicus by RNA-seq. To better address the functional role of sea cucumber circRNAs, circ432 was first found to be significantly induced by Vibrio splendidus challenge and LPS exposure in this study. Knock-down circ432 could depress the V. splendidus-induced coelomocytes phagocytosis. Moreover, circ432 is validated to serve as the sponge of miR-2008, a differential expressed miRNA in SUS-diseased sea cucumbers, by Argonaute 2-RNA immunoprecipitation (AGO2-RIP) assay, luciferase reporter assay and RNA fluorescence in situ hybridization (FISH) in vitro. Engulfment and cell motility protein 1 (AjELMO1) is further demonstrated to be the target of miR-2008, and silencing AjELMO1 inhibits the V. splendidus-induced coelomocytes phagocytosis, and this phenomenon could be further suppressed by supplementing with miR-2008 mimics, suggesting that circ432 might regulate coelomocytes phagocytosis via miR-2008-AjELMO1 axis. We further confirm that the depressed coelomocytes' phagocytosis by circ432 silencing is consistent with the decreased abundance of AjELMO1, and could be recovered by miR-2008 inhibitors transfection. All our results provide the evidence that circ432 is involved in regulating pathogen-induced coelomocyte phagocytosis via sponge miR-2008 and promotes the abundance of AjELMO1. These findings will enrich the regulatory mechanism of phagocytosis in echinoderm and provide theoretical data for SUS disease prevention and control in sea cucumbers.

The Tsetse Metabolic Gambit: Living on Blood by Relying on Symbionts Demands Synchronization

Tsetse flies have socioeconomic significance as the obligate vector of multiple Trypanosoma parasites, the causative agents of Human and Animal African Trypanosomiases. Like many animals subsisting on a limited diet, microbial symbiosis is key to supplementing nutrient deficiencies necessary for metabolic, reproductive, and immune functions. Extensive studies on the microbiota in parallel to tsetse biology have unraveled the many dependencies partners have for one another. But far less is known mechanistically on how products are swapped between partners and how these metabolic exchanges are regulated, especially to address changing physiological needs. More specifically, how do metabolites contributed by one partner get to the right place at the right time and in the right amounts to the other partner? Epigenetics is the study of molecules and mechanisms that regulate the inheritance, gene activity and expression of traits that are not due to DNA sequence alone. The roles that epigenetics provide as a mechanistic link between host phenotype, metabolism and microbiota (both in composition and activity) is relatively unknown and represents a frontier of exploration. Here, we take a closer look at blood feeding insects with emphasis on the tsetse fly, to specifically propose roles for microRNAs (miRNA) and DNA methylation, in maintaining insect-microbiota functional homeostasis. We provide empirical details to addressing these hypotheses and advancing these studies. Deciphering how microbiota and host activity are harmonized may foster multiple applications toward manipulating host health, including identifying novel targets for innovative vector control strategies to counter insidious pests such as tsetse.

AMPK-mediated glutaminolysis maintains coelomocytes redox homeostasis in Vibrio splendidus-challenged Apostichopus japonicus

Glutaminolysis has been proved to play an irreplaceable role in vertebrate immunity, including effects on cytokine production, bacterial killing, and redox homeostasis maintenance. Our previous metabolomics analysis indicated that glutaminolysis metabolic substrates glutamine (Gln) and metabolites glutamate (Glu) were significantly lower in Skin ulceration syndrome (SUS)-diseased Apostichopus japonicus. To further delineate the role of glutaminolysis, we assayed the levels of Gln and Glu. We found that their contents in coelomocytes were decreased, accompanied by an increase in glutathione (GSH) in pathogen-challenged Apostichopus japonicus. Consistently, the mRNA transcripts of three key genes in glutaminolysis (AjASCT2, AjGOT, and AjGCS) were significantly induced. Moreover, the increased MDA and NADPH/NADP ⁺ levels in response to pathogen infection indicated that oxidative stress occurs during the immune response. The metabolic regulator AMPKβ could regulate glutaminolysis in vertebrates by inducing cells to take up extracellular Gln. To explore the underlying regulatory mechanism behind glutaminolysis that occurred in coelomocytes, the full-length cDNA of AMPKβ was identified from A. japonicus (designated as AjAMPKβ). AjAMPKβ expression was significantly induced in the coelomocytes after pathogen challenge, which was consistent with the expression of key genes of glutaminolysis. A functional assay indicated that AjAMPKβ silencing by siRNA transfection could increase the levels of Gln and Glu and depress the production of GSH. Moreover, the expression of glutaminolysis-related genes was significantly inhibited, and the reduction of redox homeostasis indexes (MDA and NADPH/NADP⁺) was also observed. Contrastingly, AjAMPKβ overexpression promoted redox homeostasis balance. Intracellular ROS is mostly responsible for breaking redox homeostasis and leading to oxidative stress, contributing to cell fate changes in immune cells. Exogenous Gln and GSH treatments could significantly reduce ROS level while the AjAMPKβ silencing induced the level of ROS and accelerated the necrosis rate. All these results collectively revealed that AjAMPKβ could modulate cellular redox homeostasis by affecting the glutaminolysis in A. japonicus.

Tissue inhibitor of metalloproteinases 1 is involved in ROS-mediated inflammation via regulating matrix metalloproteinase 1 expression in the sea cucumber Apostichopus japonicus

Tissue inhibitors of metalloproteinases (TIMPs) serve as matrix metalloproteinase (MMP) inhibitors in the pathogenesis of inflammatory diseases in vertebrates. We cloned and characterised the TIMP1 gene from Apostichopus japonicus using RACE approaches (designated as AjTIMP1). For Vibrio splendidus-challenged sea cucumbers, the peak expression of AjTIMP1 mRNAs in coelomocytes was detected at 24 h (23.44-fold) and remained at high levels (4.01-fold) until 72 h. Similarly, AjTIMP1 expression was upregulated in primary coelomocytes exposed to 10 μg mL^-1 LPS. AjTIMP1 was expressed in all tissues, and the highest expression was observed in the body wall. Functional investigation revealed an imbalance in the ratio of AjMMP1/AjTIMP1 in the skin ulceration syndrome (SUS) diseased group; it was sharply up-regulated to 3.97:1 compared with the healthy group. Furthermore, when AjTIMP1 was knocked down using small interfering RNA (siRNA-KD) to 0.4-fold, AjMMP1 and AjMMP19 were upregulated to 1.99- and 1.85-fold, respectively. AjTIMP1 siRNA-KD can promote ROS production by 26.2%, whereas AjMMP1 siRNA-KD can eliminate the increase in ROS. In inflamed tissues, collagen I and III levels were decreased by 33.1% and 33.6%, respectively, in the AjTIMP1 siRNA group at 24 h AjTIMP1 was involved in the inflammatory response by mediating ROS formation and collagen degradation.

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.

BAG2 mediates coelomocyte apoptosis in Vibrio splendidus challenged sea cucumber Apostichopus japonicus

MicroRNAs (miRNAs) are closely related to the occurrence, development, and immune response of diseases. BCL2-associated athanogene 2 (BAG2) is a member of the BAG family that functions in diverse cellular processes, including cell death, differentiation, and cell division. In this study, we cloned the cDNA full-length of sea cucumber (Apostichopus japonicus) BAG2 (AjBAG2) and confirmed it is an anti-apoptotic protein in vitro and in vivo during Vibrio splendidus infection. Moreover, we identified a perfect complementarity between miR-375 and the 3'-untranslated region (UTR) sequence of AjBAG2. The miR-375 expression decreased the luciferase activity dose-dependently when co-transfected with the AjBAG2 3'-UTR-luciferase reporter containing the miR-375 target site in epithelioma papulosum cyprini (EPC) cells. This inhibition was partially recovered by a miR-375 specific inhibitor. The mRNA and protein levels of AjBAG2 were opposite to that of coelomocytes in challenged sea cucumber when treated with miR-375 mimics or inhibitors. Additionally, miR-375 expression induced coelomocytes apoptosis and blocked the anti-apoptotic activity of AjBAG2. Our data demonstrated that AjBAG2 is an anti-apoptotic protein during V. splendidus infection and this function can be inhibited by miR-375 in sea cucumbers.

Small RNA analysis of Perna viridis after exposure to Prorocentrum lima, a DSP toxins-producing dinoflagellate

Diarrheic shellfish poisoning toxins (DSP toxins) are a set of the most important phycotoxins produced by some dinoflagellates. Studies have shown that DSP toxins have various toxicities such as genotoxicity, cytotoxicity, and immunotoxicity to bivalve mollusks. However, these toxicities appear decreasing with exposure time and concentration of DSP toxins. The underlying mechanism involved remains unclear. In this study, small RNA sequencing was performed in the digestive gland of the mussel Perna viridis after exposure to DSP toxins-producing dinoflagellate Prorocentrum lima for different time periods. The potential roles of miRNAs in response and detoxification to DSP toxins in the mussel were analyzed. Small RNA sequencing of 12 samples from 72 individuals was conducted by BGISEQ-500. A total of 123 mature miRNAs were identified, including 90 conserved miRNAs and 33 potential novel miRNAs. After exposure to P. lima, multiple important miRNAs displayed some alterations. Further miRNA target prediction revealed some important genes involved in cytoskeleton, apoptosis, complement system and immune stress. qPCR demonstrated that miR-71_5, miR-750_1 and novel_mir4 were significantly up-regulated at 6 h after exposure to P. lima, while miR-100_2 was significantly down-regulated after 96 h of exposure. Accordingly, putative target genes of these differentially expressed miRNAs experienced some changes. After 6 h of DSP toxins exposure, NHLRC2 and C1q-like were significantly down-regulated. After 96 h of DSP toxins exposure, NHLRC2 was significantly up-regulated. It is reasonable to speculate that the mussel P. viridis might respond to DSP toxins through miR-750_1, novel_mir4 and miR-71_5 regulating the expression of relevant target genes involved in apoptosis, cytoskeleton, and immune response, etc. This study might provide new clues to uncover the toxic response of bivalve to DSP toxins and lay a foundation for revealing the roles of miRNAs in the environmental adaptation in shellfish.

MicroRNA-Mediated Regulation of Initial Host Responses in a Symbiotic Organ

One of the most important events in an animal's life history is the initial colonization by its microbial symbionts, yet little is known about this event's immediate impacts on the extent of host gene expression or the molecular mechanisms controlling it. MicroRNAs (miRNAs) are short, noncoding RNAs that bind to target mRNAs, rapidly shaping gene expression by posttranscriptional control of mRNA translation and decay. Here, we show that, in the experimentally tractable binary squid-vibrio symbiosis, colonization of the light organ induces extensive changes in the miRNA transcriptome. Examination of the squid genome revealed the presence of evolutionarily conserved genes encoding elements essential for the production and processing of miRNAs. At 24 h postcolonization, 215 host miRNAs were detected in the light organ, 26 of which were differentially expressed in response to the symbionts. A functional enrichment analysis of genes potentially targeted by downregulation of certain miRNAs at the initiation of symbiosis revealed two major gene ontology (GO) term categories, neurodevelopment and tissue remodeling. This symbiont-induced downregulation is predicted to promote these activities in host tissues and is consistent with the well-described tissue remodeling that occurs at the onset of the association. Conversely, predicted targets of upregulated miRNAs, including the production of mucus, are consistent with attenuation of immune responses by symbiosis. Taken together, our data provide evidence that, at the onset of symbiosis, host miRNAs in the light organ drive alterations in gene expression that (i) orchestrate the symbiont-induced development of host tissues, and (ii) facilitate the partnership by dampening the immune response.IMPORTANCE Animals often acquire their microbiome from the environment at each generation, making the initial interaction of the partners a critical event in the establishment and development of a stable, healthy symbiosis. However, the molecular nature of these earliest interactions is generally difficult to study and poorly understood. We report that, during the initial 24 h of the squid-vibrio association, a differential expression of host miRNAs is triggered by the presence of the microbial partner. Predicted mRNA targets of these miRNAs were associated with regulatory networks that drive tissue remodeling and immune suppression, two major symbiosis-induced developmental outcomes in this and many other associations. These results implicate regulation by miRNAs as key to orchestrating the critical transcriptional responses that occur very early during the establishment of a symbiosis. Animals with more complex microbiota may have similar miRNA-driven responses as their association is initiated, supporting an evolutionary conservation of symbiosis-induced developmental mechanisms.

Identification and functional characterization of natural resistance-associated macrophage protein 2 from sea cucumber Apostichopus japonicus

As a member of natural resistance-associated macrophage protein (Nramp) family, Nramp2 conservatively exists in the cell membrane across species and is essential for normal iron homeostasis in an H⁺-dependent manner. Withholding available iron represents an important host defense strategy. However, the function of Nramp2 in response to invading pathogens is largely unknown in invertebrates. In this study, a unique echinoderm Nramp2 was identified from sea cucumber Apostichopus japonicus (designated as AjNramp2). The cDNA sequence of AjNramp2 was 2360 bp, with a putative open reading frame of 1713 bp, encoding a typical Nramp domain containing protein with 570 amino acid residues. Structural analysis revealed that AjNramp2 consisted of highly conserved helix regions similar with the human Nramp2. Spatial expression analysis revealed that AjNramp2 was ubiquitously expressed in all examined tissues, with the highest level found in the intestine. Immunohistochemistry assay showed that AjNramp2 was mainly located in the cellular membrane in coelomocytes. Vibrio splendidus challenge and lipopolysaccharide (LPS) stimulation could significantly promote the expression of AjNramp2, which was consistent with the cellular iron level in coelomocytes. Moreover, when the expression of AjNramp2 was knocked down by siRNA-AjNramp2, the cellular iron level was coordinately decreased in coelomocytes under LPS stimulation. Taken together, results indicated that AjNramp2 serves as an iron transport receptor to withhold available iron and may contribute to the nutritional immunity defense system of sea cucumber.

Hypoxia-induced miR-92a regulates p53 signaling pathway and apoptosis by targeting calcium-sensing receptor in genetically improved farmed tilapia (Oreochromis niloticus)

miR-92a miRNAs are immune molecules that regulate apoptosis (programmed cell death) during the immune response. Apoptosis helps to maintain the dynamic balance in tissues of fish under hypoxia stress. The aim of this study was to explore the role and potential mechanisms of miR-92a in the liver of tilapia under hypoxia stress. We first confirmed that CaSR (encoding a calcium-sensing receptor) is a target gene of miR-92a in genetically improved farmed tilapia (GIFT) using luciferase reporter gene assays. In GIFT under hypoxia stress, miR-92a was up-regulated and CaSR was down-regulated in a time-dependent manner. Knocked-down CaSR expression led to inhibited expression of p53, TP53INP1, and caspase-3/8, reduced the proportion of apoptotic hepatocytes, and decreased the activity of calcium ions induced by hypoxia in hepatocytes. GIFT injected in the tail vein with an miR-92a agomir showed up-regulation of miR-92a and down-regulation of CaSR, p53, TP53INP1, and caspase-3/8 genes in the liver, resulting in lower serum aspartate aminotransferase and alanine aminotransferase activities under hypoxia stress. These findings suggest that stimulation of miR-92a interferes with hypoxia-induced apoptosis in hepatocytes of GIFT by targeting CaSR, thereby alleviating liver damage. These results provide new insights into the adaptation mechanisms of GIFT to hypoxia stress.

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.

The iron-sulfur protein subunit of succinate dehydrogenase is critical in driving mitochondrial reactive oxygen species generation in Apostichopus japonicus

Succinate dehydrogenase (SDH) is a mitochondrial enzyme with the unique ability to participate in both the tricarboxylic acid cycle and the electron transport chain to produce reactive oxygen species (ROS). The B subunit of SDH is required for succinate oxidation, which is critical for pro-inflammatory response. In this study, we cloned the iron-sulfur protein subunit of SDH from Apostichopus japonicus (denoted as AjSDHB) via RACE technology and explored its role in the immune system as a response to pathogen infection. The full-length cDNA of AjSDHB was 1442 bp with a complete open reading frame of 858 bp encoding 286 amino acids. Simple modular architecture research tool analysis revealed that AjSDHB contained two conserved domains, including a 2Fe-2S iron-sulfur cluster binding domain and a 4Fe-4S dicluster domain, without a signal peptide. Multiple sequence alignment demonstrated that AjSDHB shared a high degree of structural conservation and sequence identities with other counterparts from invertebrates and vertebrates. Phylogenetic analysis supported the finding that AjSDHB is a new member of the SDHB protein subfamily. Tissue distribution analysis revealed that AjSDHB was expressed in all examined tissues and particularly highly expressed in the muscles. AjSDHB transcripts were markedly induced in coelomocytes both by Vibrio splendidus challenge in vivo and lipopolysaccharide exposure in vitro. Function analysis showed that siRNA-mediated AjSDHB knockdown could substantially reduce the mitochondrial membrane potential (ΔΨm) and further decrease mitochondrial ROS production in A. japonicus coelomocytes. By contrast, AjSDHB overexpression considerably increased ΔΨm and mitochondrial ROS production of A. japonicus coelomocytes. These results supported the idea that AjSDHB is involved in the innate immunity of A. japonicus through its participation in mitochondrial ROS generation.

Fas-associated death domain (FADD) in sea cucumber (Apostichopus japonicus): Molecular cloning, characterization and pro-apoptotic function analysis

Fas-associated death domain (FADD) is an adaptor protein that functions in transferring the apoptotic signals regulated by the death receptors. In this study, a full-length cDNA of FADD homologue in sea cucumber Apostichopus japonicas (AjFADD) was cloned and characterized, and its functional roles in apoptosis investigated. In healthy sea cucumbers, AjFADD was expressed in all detected tissues, with higher levels in coelomocytes and intestine. AjFADD mRNA and protein levels were significantly expressed in coelomocytes after exposed with LPS or poly (I:C) in vitro, and challenged with Vibrio splendidus in vivo. Moreover, siRNA-mediated AjFADD knockdown in coelomocyte much decreased AjFADD mRNA and protein levels as well as the coelomocytes apoptosis levels. Furthermore, over-expression of the expression plasmid pcDNA3.1 encoding AjFADD (pcAjFADD) significantly increased the apoptosis levels in HEK293 cells. Taken together, our results support that AjFADD is a novel pro-apoptotic protein that might play key roles in defensing the bacterial and virus invasion in sea cucumber.

A novel β-catenin from Apostichopus japonicus mediates Vibrio splendidus-induced inflammatory-like response

β-catenin, an adaptor molecule in Wnt/β-catenin signaling pathway, is associated with different physiological processes such as intestinal immune, apoptosis, and inflammation-associated response. However, the function of β-catenin is still largely unknown in Apostichopus japonicus. In the present study, we cloned and characterized β-catenin gene from A. japonicus by RNA-seq and RACE approaches. The complete sequence of Ajβ-catenin consisted of a 5' UTR of 166 bp, a 3' UTR of 501 bp and an ORF of 2433 bp encoding a protein of 810 amino acids. Ajβ-catenin has a GSK-β consensus phosphorylation site of 21 amino acids located at N-terminal region and twelve Armadillo/β-catenin-like repeat (ARM) domains from 145 to 671 aa. Spatial expression analysis revealed that Ajβ-catenin mRNA levels displayed higher abundance in intestine. For Vibrio splendidus challenged sea cucumber, Ajβ-catenin transcripts reached their peak at 6 h and remained at higher levels until 24 h post infection in comparison with that of the control group. GSK-3β inhibitor treatment could induce both Ajβ-catenin and the inflammatory factors expression. Ajβ-catenin silencing could also down-regulate inflammatory factors expression. These results collectively suggested that Ajβ-catenin was a novel molecule mediate V. splendidus-induced immune response of A. japonicus via regulating the inflammatory factors expression.

Profiling of microRNAs and mRNAs in marine mussel Mytilus galloprovincialis

MicroRNAs (miRNAs) are a class of noncoding RNA molecules containing 18-24 nucleotides, and those with conserved structures are able to regulate the expression of eukaryotic genes by inhibition or enhancement of mRNA translation. However, miRNAs of the blue mussel, Mytilus galloprovincialis have not been reported. M. galloprovincialis is a primary species distributed along coastal zones worldwide. To reveal the repertoire of miRNAs in M. galloprovincialis, we constructed small RNA libraries prepared from three different mussels, which were then sequenced by Solexa deep sequencing technology. A total of 32,836,817, 33,359,113 and 33,093,562 clean reads from the tissues of the three M. galloprovincialis were obtained. Based on sequence similarities and hairpin structure predictions, 137 M. galloprovincialis miRNAs (mg-miRNA) were identified. Among the mg-miRNAs, 104 were conserved across species, whereas 33 might be novel and specific for M. galloprovincialis. Some of the mg-miRNAs, such as let-7 and the miR-100 family are playing key roles in many metabolic pathways and are worthy of further study. By performing a whole genome-scale characterization of mg-miRNAs and proposing their potential functions, these results provide a foundation for understanding the biological processes of the blue mussel, M. galloprovincialis.

A cyclophilin A (CypA) from Apostichopus japonicus modulates NF-κB translocation as a cofactor

As a ubiquitously expressed protein, cyclophilin A (CypA) is involved in a variety of pathological process, including immune suppression, inflammation, cell apoptosis, viral infection and stress response. However, the functional roles of CypA were largely unknown in economic marine animals. In this report, a novel CypA gene from sea cucumber Apostichopus japonicus (designated as AjCypA) was cloned and its function roles in immune responses were explored. The full-length cDNA of AjCypA was 1297 bp containing an open reading frame of 489 bp encoding a putative protein of 162 amino acids (aa). A conserved cyclophilin-like domain (CLD) with PPIase signature was located from 5 to 155 aa sequences in AjCypA, in which five necessary aa residues was totally conserved. In healthy sea cucumbers, AjCypA was expressed in all detected tissues, with highly expressed in muscles and weakly expressed in coelomocytes. AjCypA transcripts was significantly induced 8.08-fold and 5.65-fold in coelomocytes when sea cucumbers challenged with Vibrio splendidus in vivo and LPS in vitro, respectively. The expression pattern is similar with the expression of AjRel in the same condition. Moreover, GST pull-down and immunofluorescence analysis both revealed that AjCypA might be interacted with AjRel. Furthermore, AjCypA knockdown not only inhibited the expression of inflammation cytokines, but also suppressed the translocation of AjRel in nucleus induced by LPS. Taken together, our results suggested that AjCypA play key roles in V. splendidus mediated immune responses via suppressing the nuclear translocation of AjRel activity in sea cucumber.

MYC regulates coelomocytes apoptosis by targeting Bax expression in sea cucumber Apostichopus japonicus

Myelocytomatosis viral oncogene (MYC), a multifunctional transcription factor, (TF) exerts various physiological and pathological effects on animals. AjMYC could induce coelomocyte apoptosis in Apostichopus japonicus, but the underlying molecular mechanism remains poorly understood. In this study, the promoter sequence of apoptosis regulator Bcl-2-associated X (Bax) was cloned by genomic walking. The AjBax promoter region spaning 1189 bp, containing several transcription factor binding sites, included four potential E-boxes (-1030 bp to -1019 bp, -785 bp to -774 bp, -570 bp to -559 bp, -100 bp to -89 bp), two P53 binding sites (-439 bp to -430 bp, -845 bp to -836 bp), and one NF-κB site (-191 bp to -182 bp). Transient transfection of EPC cells with 5'-deletion constructs linked to luciferase reporter revealed that the region -1189/+454 contributed importantly to the expression of the AjBax. In addition, the AjBax promoter was induced by LPS, PGN or MAN. The four potential MYC binding sites were cotransfected with AjMYC in EPC cell whether AjMYC could activate AjBax expression as a transcriptional factor. Only P1 (-1189/+454) fragment containing the first MYC binding site transfection increased the luciferase activity by 2.08-fold (p < 0.01) compared with the control. The first MYC binding site -1030/-1019 was essential to induce AjBax transcription. Further functional assay indicated that AjBax was significantly induced by 3.54-fold increase (p < 0.01) after AjMYC overexpression in sea cucumber coelomocytes. All our findings supported that AjMYC could regulate coelomocyte apoptosis by directly targeting AjBax expression in A. japonicus.

Bcl-2 mediates coelomocytes apoptosis by suppressing cytochrome c release in Vibrio splendidus challenged Apostichopus japonicus

Apoptosis is an evolutionarily conserved immune response and plays a fundamental role in many physiological processes. In this study, the important apoptosis regulator of Bcl-2 homolog from economic marine animal Apostichopus japonicus (AjBcl-2) was cloned and its roles in V. splendidus infection explored. The AjBcl-2 gene contains 3263 nucleotides, with a 5' UTR of 519 bp, an ORF of 660 bp encoding 219 aa sequences, and a 3' UTR of 2084 bp. The AjBcl-2 protein shared a conserved Bcl domain and three Bcl-2 homology domains by SMART program. In healthy sea cucumbers, AjBcl-2 mRNA was expressed in all examined tissues with the peak expression in coelomocytes. The mRNA and protein levels of AjBcl-2 in coelomocytes were depressed at 12 h and 24 h, and induced at 48 h post V. splendidus challenge. In the same conditions, coelomocytes apoptosis rates were significantly increased at 24 h and decreased at 48 h. Moreover, siRNA-mediated AjBcl-2 knockdown significantly increased the coelomocytes apoptosis rates, which could be partially recovered by recombinant AjBcl-2 administration. Furthermore, there was an increase in the AjCyt c protein expression coupled with the downregulation expression of AjBcl-2 post AjBcl-2 silencing. Our results suggested that AjBcl-2 suppressed apoptosis by preventing the AjCyt c release in coelomocytes, and thus mediating V. splendidus infection in sea cucumbers.

Bax functions as coelomocyte apoptosis regulator in the sea cucumber Apostichopus japonicus

Bcl-2-associated X (Bax) belongs to the Bcl-2 protein family and its pro-apoptotic function has been confirmed in many vertebrate species. However, the functional role of Bax in apoptosis in invertebrates is limited. Here, a Bax homologue (AjBax) in Apostichopus japonicas was cloned and characterized, and its pro-apoptotic function explored. In healthy sea cucumbers, AjBax was expressed in coelomocyte with the highest levels. AjBax mRNA and protein levels were significantly induced in coelomocytes post Vibrio splendidus challenge in vivo and LPS-exposed in vitro. Moreover, siRNA-mediated AjBax knockdown in coelomocyte significantly decreased AjBax mRNA and protein levels as well as the apoptosis levels of coelomocyte. Furthermore, AjBax protein levels and coelomocyte apoptosis levels could be partially recovered to their original levels after supplementation with recombinant AjBax. Our results support that AjBax has a similar function to Bax proteins in vertebrates and that it may serve as a pro-apoptotic regulator in sea cucumbers.

microRNA-92a regulates the expression of aphid bacteriocyte-specific secreted protein 1

OBJECTIVE

Aphids harbor a nutritional obligate endosymbiont in specialized cells called bacteriocytes, which aggregate to form an organ known as the bacteriome. Aphid bacteriomes display distinct gene expression profiles that facilitate the symbiotic relationship. Currently, the mechanisms that regulate these patterns of gene expression are unknown. Recently using computational pipelines, we identified miRNAs that are conserved in expression in the bacteriomes of two aphid species and proposed that they function as important regulators of bacteriocyte gene expression. Here using a dual luciferase assay in mouse NIH/3T3 cell culture, we aimed to experimentally validate the computationally predicted interaction between Myzus persicae miR-92a and the predicted target region of M. persicae bacteriocyte-specific secreted protein 1 (SP1) mRNA.

RESULTS

In the dual luciferase assay, miR-92a interacted with the SP1 target region resulting in a significant downregulation of the luciferase signal. Our results demonstrate that miR-92a interacts with SP1 to alter expression in a heterologous expression system, thereby supporting our earlier assertion that miRNAs are regulators of the aphid/Buchnera symbiotic interaction.

Macrophage migration inhibitory factor is involved in inflammation response in pathogen challenged Apostichopus japonicus

Macrophage migration inhibitory factor (MIF) is a cytokine and plays critical roles in inflammatory and immune responses in vertebrates. However, its functional role in inflammation has not been well studied in invertebrates. In the present study, we cloned and characterized MIF gene from Apostichopus japonicus by RNA-seq and RACE approaches (designated as AjMIF). A 1047 bp fragment representing the full-length cDNA of AjMIF was obtained, including a 5' UTR of 100 bp, an open reading frame (ORF) of 366 bp encoding a polypeptide of 121 amino acids residues with the molecular weight of 13.43 kDa and theoretical isoelectric point of 5.63 and a 3' UTR of 580 bp. SMART analysis showed that AjMIF has conserved MIF domain (2-117aa) similar to its mammalian counterparts. The amino terminal proline residue (P²) and invariant lysine residue (K³³) which are critical active sites of tautomerase activity in mammalian MIF were also detected. Phylogenic analysis and multiple alignments have shown that AjMIF shared higher degree of structural conservation and sequence identities with other counterparts from invertebrates and vertebrates. For Vibrio splendidus challenged sea cucumber, the peak expression of AjMIF mRNAs in coelomocytes were detected at 6 h (23.5-fold) and remained at high levels until 24 h (4.01-fold), and returned to normal level at 48 h in comparison with that of the control group. Similarly, a significant increase in the relative mRNA levels of AjMIF was also found in 10 μg mL^-1 LPS-exposed primary cultured coelomocytes. Functional analysis indicated that recombinant AjMIF incubation could promote inflammatory response related genes of Ajp105, AjVEGF, AjMMP1 and AjHMGB3 expression by 1.35-fold, 1.36-fold, 1.83-fold and 1.27-fold increase, respectively, which was consistent with the findings in vertebrate MIFs. All these results collectively suggested that AjMIF had a similar function to MIFs in higher animals and might serve as a candidate cytokine in inflammatory regulation in sea cucumber.

VEGF-like protein from Apostichopus japonicus promotes cell proliferation and migration

Vascular endothelial growth factor (VEGF) is a key conservative regulator of inflammation response by promoting cell proliferation, migration, and vascular permeability. It also induces the release of inflammatory factors in vertebrates. We previously characterized NLR family pyrin domain containing 3 and HMGB3 homology in Apostichopus japonicus, providing the occurrence of inflammation in this species. However, to our knowledge, other inflammation-related molecules, such as VEGF, have rarely been investigated. In the present study, a novel VEGF homolog was identified from A. japonicus (designated as AjVEGF) by rapid amplification of cDNA ends. Full-length cDNA of AjVEGF was 3181 bp with a putative open reading frame of 1752 bp encoding 583 amino acid (aa) residue protein. Structural analysis revealed that AjVEGF processed characteristic VEGF domains of platelet-derived growth factor domain (132-232 aa) and CXC domain (223-270 aa). Multiple sequence alignment and phylogenetic analysis both supported that AjVEGF belongs to a new member of VEGF protein subfamily. Both Vibrio splendidus challenge in vivo and lipopolysaccharide stimulation in vitro could significantly upregulate mRNA expression of AjVEGF compared with the control group. Functional analysis indicated that recombinant AjVEGF promoted coelomocyte proliferation and migration not only in sea cucumber but also in human colorectal adenocarcinoma cells (HT29). This consistent function was also detected for human VEGFs. Taken together, these findings suggest that AjVEGF has a similar function of VEGF in higher animals and might serve as a candidate cytokine in sea cucumber inflammation.

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.

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.

In-depth profiling of miRNA regulation in the body wall of sea cucumber Apostichopus japonicus during skin ulceration syndrome progression

MicroRNAs (miRNAs) are small non-coding RNAs that mediate mRNA degradation or translation repression. Previous study showed that the expression of miRNAs was significantly changed in the body wall of sea cucumber Apostichopus japonicus after skin ulceration syndrome (SUS) infection, which is a dynamic process. However, the critical miRNAs from body wall that involved in different infection stages of SUS remain unknown. In this study, four cDNA libraries were constructed with the body wall from healthy and three SUS-infected stages of A. japonicus. A total of 248 conserved miRNAs and five novel miRNAs were identified through Illumina HiSeq 2000 platform. Compared to the control, 238 miRNAs showed significant differential expression at three stages of SUS progression. Totally, 3149 miRNA-mRNA pairs were identified by target prediction and 314 miRNA-mRNA pairs showed negative correlation. It is noteworthy that 15 miRNAs and four mRNAs were located at the crucial positions of the network built with the anti-correlated miRNA-mRNA pairs. GO and KEGG enrichment analysis indicated that the predicted targets were involved in many immune-related processes. Deep analysis of miR-31c-5p, miR-29b-3p, NF-kB, mucin 2 and titin showed that they may play important roles in the pathogens attachment and recognition, signaling transduction and lesions repair of A. japonicus after SUS infection. These results would be useful for further investigating the potential roles of critical miRNAs and mRNAs in A. japonicus immune regulation.

microRNA regulation in an ancient obligate endosymbiosis

Although many insects are associated with obligate bacterial endosymbionts, the mechanisms by which these host/endosymbiont associations are regulated remain mysterious. While microRNAs (miRNAs) have been recently identified as regulators of host/microbe interactions, including host/pathogen and host/facultative endosymbiont interactions, the role miRNAs may play in mediating host/obligate endosymbiont interactions is virtually unknown. Here, we identified conserved miRNAs that potentially mediate symbiotic interactions between aphids and their obligate endosymbiont, Buchnera aphidicola. Using small RNA sequence data from Myzus persicae and Acyrthosiphon pisum, we annotated 93 M. persicae and 89 A. pisum miRNAs, among which 69 were shared. We found 14 miRNAs that were either highly expressed in aphid bacteriome, the Buchnera-housing tissue, or differentially expressed in bacteriome vs. gut, a non-Buchnera-housing tissue. Strikingly, 10 of these 14 miRNAs have been implicated previously in other host/microbe interaction studies. Investigating the interaction networks of these miRNAs using a custom computational pipeline, we identified 103 miRNA::mRNA interactions shared between M. persicae and A. pisum. Functional annotation of the shared mRNA targets revealed only two over-represented cluster of orthologous group categories: amino acid transport and metabolism, and signal transduction mechanisms. Our work supports a role for miRNAs in mediating host/symbiont interactions between aphids and their obligate endosymbiont Buchnera. In addition, our results highlight the probable importance of signal transduction mechanisms to host/endosymbiont coevolution.

Integrative mRNA-miRNA interaction analysis associate with immune response of sea cucumber Apostichopus japonicus based on transcriptome database

MicroRNAs (miRNAs) constitute a family of endogenous non-coding small RNAs that have been demonstrated to be the key effectors in mediating host-pathogen interactions. Additionally, high-throughput sequencing provides unexampled opportunities to identify the pathogenic mechanism underlying miRNAs. In the present study, the target genes of immune-related miRNAs (miR-31, miR-2008, miR-92a, miR-210 and miR-7) and specific miRNAs (miR-2004) in Echinodermata were predicted in silico and validated. Gene ontology (GO) analysis of the target genes of these six miRNAs were conducted to further understand the regulatory function in the host immunity of Apostichopus japonicus (A. japonicus). Among the putative target genes of the six miRNAs, various immune-related targets were annotated, such as Nephl, SEC14Ll, p105, GL2, LYS, FNIAL, mTOR, LITAF, SLC44, TLR3, Apaf-1, and CNTN4. This work will provide valuable genetic resources to understand the interaction of multiple mRNA-miRNAs and the regulation mechanism in the anti-bacterial process in the sea cucumber.

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.

Transcriptome-wide analysis of microRNAs in Branchiostoma belcheri upon Vibrio parahemolyticus infection

MicroRNAs (miRNAs) are endogenous small non-coding RNAs that participate in diverse biological processes via regulating expressions of target genes at post-transcriptional level. Amphioxus, as modern survivor of an ancient chordate lineage, is a model organism for comparative genomics study. However, miRNAs involved in regulating immune responses in Branchiostoma belcheri are largely unclear. Here, we systematically investigated the microRNAs (miRNAs) involved in regulating immune responses in the cephalochordate amphioxus (Branchiostoma belcheri) through next-generation deep sequencing of amphioxus samples infected with Vibrio parahemolyticus. We identified 198 novel amphioxus miRNAs, consisting of 12 conserved miRNAs, 33 candidate star miRNAs and 153 potential amphioxus-specific-miRNAs. Using microarray profiling, 14 miRNAs were differentially expressed post infection, suggesting they are immune-related miRNAs. Eight miRNAs (bbe-miR-92a-3p, bbe-miR-92c-3p, bbe-miR-210-5p, bbe-miR-22-3p, bbe-miR-1∼bbe-miR-133 and bbe-miR-217∼bbe-miR-216 clusters) were significantly increased at 12 h post-infection, while bbe-miR-2072-5p was downregulated at 6 h and 12 h. Three miRNAs, bbe-miR-1-3p, bbe-miR-22-3p and bbe-miR-92a-3p, were confirmed to be involved in immune responses to infection by qRT-PCR. Our findings further clarify important regulatory roles of miRNAs in the innate immune response to bacterial infection in amphioxus.

Characterization of NLRP3-like gene from Apostichopus japonicus provides new evidence on inflammation response in invertebrates

Inflammatory/defensive response after pathogen invasion is considered a local defense reaction in vertebrates. Inflammation response in Apostichopus japonicus was hardly determined due to scarce information available for nucleotide binding domain-like receptor family, pyrin domain-containing (NLRP) family. In the present study, invertebrate NLRP homologue was identified from A. japonicus (designated as AjNLRP3-like) by rapid amplification of cDNA ends. Full-length cDNA of AjNLRP3-like measured 2970 bp with 2265 bp open reading frame encoding a 754-amino acid (aa) residue protein. Structural analysis revealed that AjNLRP3-like processed characteristic domains of pyrin (32-102aa) and NACHT (183-339aa). Multiple sequence alignment and phylogenetic analysis supported that AjNLRP3-like belongs to a new member of NLRP3 protein subfamily. Spatial expression analysis revealed that AjNLRP3-like was ubiquitously expressed in all examined tissues with larger magnitude in coelomocytes. Both Vibrio splendidus challenge in vivo and lipopolysaccharide stimulation in vitro significantly upregulated mRNA expression of AjNLRP3-like when compared with the control group. NLRP3-mediated inflammation response depended on release of lysosomal cathepsin B (CTSB) and subsequent activation of high-mobility group box (HMGB) in vertebrates. We investigated expression profiles of AjNLRP3-like and AjHMGB after AjCTSB knock-down and discovered that AjNLRP3-like was depressed by 0.66-fold and 0.47-fold, whereas AjHMGB was depressed by 0.70-fold and 0.50-fold at 24 and 48 h in AjCTSB-silenced group, respectively. Similarly, down-regulation of AjHMGB was also observed after AjNLRP3-like knock-down. This study therefore suggests that A. japonicus feature similar inflammatory events as those in vertebrates, and activation of AjNLRP3-like depends on AjCTSB expression and release of AjHMGB.

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.

Inhibition of miR-92d-3p enhances inflammation responses in genetically improved farmed tilapia (GIFT, Oreochromis niloticus) with Streptococcus iniae infection by modulating complement C3

MicroRNAs (miRNAs) are small, non-coding RNAs that regulate target gene expression by binding to the 3'-untranslated regions (3'-UTRs) of their target mRNAs. The miR-92 family is an important miRNA family, which was discovered to be related to regulation of tumor proliferation, apoptosis, invasion, and metastasis. Inhibition of miR-92d-3p was found previously in head kidney of genetically improved farmed tilapia (GIFT, Oreochromis niloticus) exposed to Streptococcus iniae infection. In this study, we found that miR-92d-3p regulated complement C3 mRNA levels by binding to its 3'-UTR by 3'-UTR luciferase reporter assay, and reduced miR-92d-3p expression resulted in increased C3 mRNA levels. We detected a negative relationship between the expression levels of miR-92d-3p and C3 in GIFT injected with miRNA antagomir. We performed in vivo functional analysis by miR-92d-3p silencing. Inhibition of miR-92d-3p levels in GIFT head kidney caused a significant increase in C3 expression, which consequently increased the white blood cell counts and interleukin-1β, tumor necrosis factor-α, and interferon-γ mRNA levels, all of which may help to activate the inflammatory response in GIFT post-infection with S. iniae. Our findings indicate that miR-92d-3p regulated C3 levels by binding with the C3 mRNA 3'-UTR, and this interaction affected S. iniae infection induction and the immune response in GIFT. We concluded that miR-92d-3p plays an important role in modulating the inflammatory response in GIFT head kidney. Our findings may contribute to understanding the mechanisms of miRNA-mediated gene regulation in tilapia in response to S. iniae infection.

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.

Effects of exposure to Streptococcus iniae on microRNA expression in the head kidney of genetically improved farmed tilapia (Oreochromis niloticus)

Background

Genetically improved farmed tilapia (GIFT, Oreochromis niloticus) are susceptible to infection by Streptococcus iniae when maintained in modern intensive culture systems. GIFT are commercially important fishes that are cultured widely in southern China. The role of microRNAs (miRNAs) in the regulatory response of GIFT to S. iniae infection has been underestimated and has not yet been well studied. Head kidney has an important immune function in teleost fishes. The main aim of this study was to determine the possible function of miRNAs in head kidney of S. iniae-infected GIFT. MiRNAs are small, non-coding RNAs that regulate gene expression by binding to the 3’-untranslated regions of their target mRNAs. MiRNAs are known to regulate immune-regulated signaling and inflammatory response pathways.

Results

High-throughput deep sequencing of two libraries (control group [CO] and infected group [IN]) of RNA extracted from GIFT head kidney tissues generated 12,089,630 (CO) and 12,624,975 (IN) clean reads. Bioinformatics analysis identified 1736 and 1729 conserved miRNAs and 164 and 165 novel miRNAs in the CO and IN libraries, respectively. Three miRNAs (miR-310-3p, miR-92, and miR-127) were found to be up-regulated and four miRNAs (miR-92d-3p, miR-375-5p, miR-146-3p, and miR-694) were found to be down-regulated in the S. iniae-infected GIFT. The expressions of these miRNAs were verified by quantitative real-time PCR. RNAhybrid and TargetScan were used to identify complementary miRNA and mRNA target sites, and the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases were used to annotate and predict potential downstream regulation of biological pathways. Seven target genes, which encode immune-related proteins (complement C3, cytidine deaminase, regulator of G-protein Rgs22, mitogen-activated protein kinase Mapk1, metabotropic glutamate receptorm GluR8, calcium-sensing receptor CaSR, and microtubule-associated protein Map1S) were predicted to play crucial roles in the GIFT response to S. iniae infection.

Conclusions

S. iniae outbreaks have hindered the development of the tilapia industry in China. Understanding the miRNA transcriptome of S. iniae-infected GIFT is important for exploring the immune responses regulated by miRNAs as well as for studying novel regulated networks to prevent and treat S. iniae infections in the future.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3591-z) contains supplementary material, which is available to authorized users.

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.

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.

Expression analysis of microRNAs related to the skin ulceration syndrome of sea cucumber Apostichopus japonicus

MicroRNAs (miRNAs) are small non-coding RNAs that are involved in many biological processes. To investigate the miRNAs related to skin ulceration syndrome (SUS) of Apostichopus japonicus, small RNA libraries of body wall, intestine, respiratory tree and coelomocytes from healthy and diseased A. japonicus were sequenced on Illumina Hiseq 2000 platform. A total of 247 conserved and 10 novel miRNAs were identified across all libraries. After pair-wise comparisons, 215 miRNAs in body wall, 36 in intestine, 2 in respiratory tree and 38 in coelomocytes showed significant expression differences. Further analyses were conducted on some tissue-specific differentially expressed miRNAs: miR-8 and miR-486-5p in body wall, miR-200-3p, let-7-5p and miR-125 in intestine, miR-278a-3p and bantam in respiratory, miR-10a and miR-184 in coelomocytes. Notably, these miRNAs in some species were reported to function in various physiological or pathological processes associated with immune regulations. Using stem-loop quantitative real time PCR, six representative miRNAs in four tissues were selected to validate the sequencing results. The Pearson's correlation coefficient (R) of the six miRNAs ranged from 0.777 to 0.948, which confirmed the consistency and accuracy between these two approaches. This study provides comprehensive expression and regulation patterns of functional miRNAs in different tissues and gives insights into the tissue-specific immune response mechanisms in SUS-infected A. japonicus.

Nemo like kinase negatively regulates NF-κB activation and coelomocytes apoptosis in Apostichopus japonicus

Nuclear factor kappa B (NF-κB) transcription factors are related to several physiological processes, including innate and acquired immunity. In this study, a novel negative regulator of the Nemo-like kinase (NLK) gene was identified from Apostichopus japonicus through PCR (denoted as AjNLK). The complete AjNLK cDNA was of 2335 bp, with a 5'-UTR of 315 bp, a 3'-UTR of 718 bp, and a putative ORF of 1302 bp, and encoded a polypeptide of 433 amino acid residues with a typical serine/threonine protein kinase domain. Blast analysis revealed that AjNLK shared a high degree of structural conservation with its counterparts from other invertebrates and vertebrates. Spatial expression analysis indicated that the expression of AjNLK mRNA transcripts was higher in the tentacles than that in coelomocytes. The expression of AjNLK mRNA in coelomocytes was suppressed after Vibrio splendidus challenge by 0.51-fold and 0.41-fold at 72 and 96 h, respectively, compared with that in the control group. Similarly, AjNLK expression was down-regulated in primary coelomocytes exposed to 1 μg mL(-1) lipopolysaccharide (LPS). Functional investigation further revealed that the NF-κB factor p105 was induced at both mRNA and protein levels after AjNLK silencing in vitro. Meanwhile, the apoptosis of LPS-induced coelomocytes was significantly inhibited in AjNLK siRNA-transfected coelomocytes. These results supported that AjNLK negatively regulated NF-κB activation and cell apoptosis in sea cucumber.

MiR-200 modulates coelomocytes antibacterial activities and LPS priming via targeting Tollip in Apostichopus japonicus

In order to explore the potential roles of microRNAs (miRNAs) in regulating Toll-like receptor (TLR) pathways, we identified Toll interacting protein as a putative target of miR-200 in Apostichopus japonicus coelomocytes by RNA-seq screening (denoted as AjTollip). The positive expression profiles of miR-200 and AjTollip were detected in both LPS exposure primary coelomocytes and Vibrio splendidus challenge sea cucumber. Co-infection miR-200 mimics significantly elevated the expression of AjTollip and its down-stream molecules. In contrast, miR-200 inhibitor significantly repressed the expression of these TLR-pathway members. More importantly, miR-200 displayed not only to enhance coelomocytes antibacterial activities, but to suppress LPS priming in vitro. Overall, all these results will enhance our understanding on miR-200 regulatory roles in anti-bacterial process in sea cucumber.