Identification, functional characterization and expression pattern of interferon-gamma (IFN-γ) and interferon-gamma receptor 1 (IFNGR1) in Nibea albiflora

Interferon-gamma (IFN-γ) is an inflammatory cytokine that plays a crucial role in regulating both innate and cell-mediated immune responses by binding to a receptor complex made up of IFNGR1 and IFNGR2. In this study, the complete cDNA of IFN-γ and IFNGR1 from Nibea albiflora were cloned and functionally characterized (named NaIFN-γ and NaIFNGR1), whose complete cDNA sequences were 1593 bp and 2792 bp, encoding 201 and 399 amino acids, respectively. Multiple sequence alignment and phylogenetic analysis showed that the concluded amino acids sequences of NaIFN-γ and NaIFNGR1 shared high identity with their teleost orthologues including the IFN-γ signature and nuclear localization signal (NLS) motif in NaIFN-γ and FN Ⅲ domain in NaIFNGR1. Real-time PCR showed that NaIFN-γ and NaIFNGR1 constitutively expressed in all tested tissues, such as the head-kidney, spleen, liver, kidney, gill, muscle, blood, and intestine with the highest expression of NaIFN-γ and NaIFNGR1 appearing in the liver and gill, respectively. After experiencing stimulation with Polyinosinic-polycytidylic acid (Poly (I:C)), Vibrio alginolyticus (V. alginolyticus) or Vibrio parahaemolyticus (V. parahaemolyticus), NaIFN-γ and NaIFNGR1 mRNA were up-regulated with the time-dependent model. Due to the presence of a nuclear localization signal (NLS), the subcellular localization revealed that NaIFN-γ dispersed throughout the cytoplasm and nucleus. NaIFNGR1, as a member of Cytokine receptor family B, was primarily expressed on the cell membrane. When NaIFN-γ and NaIFNGR1 were co-transfected, their fluorescence signals overlapped on the membrane of HEK 293T cells indicating the potential interaction between IFN-γ and IFNGR1. The GST-pull-down results further showed that NaIFN-γ could directly interact with the extracellular region of NaIFNGR1, further confirming the affinity between IFN-γ and IFNGR1. Taken together, the results firstly demonstrated that the NaIFN-γ ligand-receptor system existed in N.albiflora and played a pivotal part in N.albiflora's immune response against pathogenic bacterial infections, which contributed to the better understanding of the role of IFN-γ in the immunomodulatory mechanisms of teleost.

Reparative effect of different dietary additives on soybean meal-induced intestinal injury in yellow drum (Nibea albiflora)

Soybean meal (SBM) is an acceptable replacement for unsustainable marine fish meal (FM) in aquaculture. However, we previously reported that high dietary SBM supplementation causes intestinal inflammatory injury in yellow drum (Nibea albiflora). Accordingly, a 4-week SBM-induced enteritis (SBMIE) in yellow drum trial was conducted first, followed by a 4-week additive-supplemented reparative experiment to evaluate the reparative effect of five additives on SBMIE in yellow drum. The control diet comprised 50% FM protein substituted with SBM. The additive-supplemented diet was added with 0.02% curcumin (SBMC), 0.05% berberine (SBM-BBR), 0.5% tea polyphenols (SBM-TPS), 1% taurine (SBM-TAU), or 0.8% glutamine (SBM-GLU) based on the control diet, respectively. The weight gain (WG), specific growth rate (SGR), feed efficiency ratio (FER), and survival rate (SR) of fish fed the additive-supplemented diets were significantly higher than those of fish fed the SBM diet. The WG, SGR, and FER of fish fed the SBMC, SBM-GLU and SBM-TAU diets were significantly higher than those of fish fed other diets. Moreover, fish fed the additive-supplemented diets SBMC and SBM-GLU, exhibited significantly increased intestinal villus height (IVH), intestinal muscular thickness (IMRT), and intestinal mucosal thickness (IMLT) and significantly decreased crypt depth (CD) in comparison with those fed the SBM diets. The relative expression of intestinal tight junction factors (ocln, zo1), cytoskeletal factors (f-actin, arp2/3), and anti-inflammatory cytokines (il10, tgfb) mRNA was remarkably elevated in fish fed additive-supplemented diets than those of fish fed the SBM diet. Whereas, the relative expression of intestinal myosin light chain kinase (mlck) and pro-inflammatory cytokines (il1, il6, tnfa) mRNA was markedly lower in fish fed the additive-supplemented diets. The highest relative expression of intestinal ocln, f-actin, and arp2/3 and the lowest relative expression of intestinal mlck were found in fish fed the SBMC diet. Hence, all five dietary additives effectively repaired the intestinal injury induced by SBM, with curcumin exhibiting the strongest repair effect for SBMIE in yellow drum.

Cloning, subcellular localization and antibacterial functional analysis of NK-lysin in yellow drum (Nibea albiflora)

Vibrio harveyi is the primary pathogenic bacteria affecting Nibea albiflora aquaculture. In a previous phase, our laboratory intentionally exposed N. albiflora to V. harveyi and analyzed the outcomes using a combination of genome-wide association study (GWAS) and RNA-seq. The results revealed that the antimicrobial peptide NK-lysin (YdNkl-1) was a candidate gene for resistance to V. harveyi disease in N. albiflora. To investigate the role of the antimicrobial peptide NK-lysin in N. albiflora's antimicrobial immunity, we screened the YdNkl-1 gene from the transcriptome database. The full-length cDNA of YdNkl-1 gene is 508 bp, with an open reading frame (ORF) of 477 bp, encoding 158 amino acids. The deduced amino acid sequence of YdNkl-1 contains a signal peptide (1st-22nd amino acids) and a Saposin B domain (50th-124th amino acids), akin to mammalian NK-lysin. Phylogenetic tree analysis confirmed that the NK-lysin of teleost fish clustered into a single species, and YdNkl-1 was most closely related to Larimichthys crocea. Subcellular localization showed that YdNkl-1 was distributed in cytoplasm and nucleus of yellow drum kidney cells. Furthermore, YdNkl-1 mRNA transcripts were significantly up-regulated in the skin, gill, intestine, head-kidney, liver, and spleen after V. harveyi infection, suggesting a critical role in N. albiflora's defense against V. harveyi infection. Additionally, we purified and observed the YdNkl-1 protein, which exhibited a potent membrane-disrupting effect on V. harveyi, Pseudomonas plecoglossicida, Vibrio parahaemolyticus, Escherichia coli and Bacillus subtilis. These findings underscore the significance of NK-lysin in N. albiflora's resistance to V. harveyi infection and provide new insights into the crucial role of NK-lysin in the innate immunity of teleost fishes.

Spleen Transcriptome Profiling Reveals Divergent Immune Responses to LPS and Poly (I:C) Challenge in the Yellow Drum (Nibea albiflora)

The yellow drum (Nibea albiflora) is a marine teleost fish with strong disease resistance, yet the understanding of its immune response and key functional genes is fragmented. Here, RNA-Seq was used to investigate the regulation pathways and genes involved in the immune response to infection with lipopolysaccharide (LPS) and polyinosinic-polycytidylic acid (poly (I:C)) on the spleen of the yellow drum. There were fewer differentially expressed genes (DEGs) in the LPS-infected treatment group at either 6 or 48 h. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that these DEGs were mainly significantly enriched in c5-branching dibasic acid metabolic and complement and coagulation cascades pathways. The yellow drum responded more strongly to poly (I:C) infection, with 185 and 521 DEGs obtained under 6 and 48 h treatments, respectively. These DEGs were significantly enriched in the Toll-like receptor signaling pathway, RIG-I-like receptor signaling pathway, Jak-STAT signaling pathway, NOD-like signaling pathway, and cytokine-cytokine receptor interaction. The key functional genes in these pathways played important roles in the immune response and maintenance of immune system homeostasis in the yellow drum. Weighted gene co-expression network analysis (WGCNA) revealed several important hub genes. Although the functions of some genes have not been confirmed, our study still provides significant information for further investigation of the immune system of the yellow drum.

Autochthonous Bacillus subtilis and Enterococcus faecalis improved liver health, immune response, mucosal microbiota and red-head disease resistance of yellow drum (Nibea albiflora)

Yellow drum (Nibea albiflora), a commercially important fish species in the coastal regions of southeast China, is highly susceptible to red-head disease caused by Vibrio harveyi B0003. Probiotics have been shown to enhance disease resistance in fish, but whether commensal probiotics could improve of the resistance to red-head disease in yellow drum and possible mechanisms has yet not been reported. A six-week feeding trial was conducted to investigate the red-head disease resistance potentials of five probiotic candidates (Bacillus megaterium B1M2, B. subtilis B0E9, Enterococcus faecalis AT5, B. velezensis DM5 and B. siamensis B0E14), and the liver health, serum and skin immunities, gut and skin mucosal microbiota of yellow drum were determined to illustrate the possible mechanisms. The results showed that autochthonous B. subtilis B0E9 and E. faecalis AT5 (particularly E. faecalis AT5, P < 0.05) effectively improved red-head disease resistance in yellow drum. Furthermore, B. subtilis B0E9 and E. faecalis AT5 (particularly E. faecalis AT5) efficiently improve liver health by improving liver morphology and decreasing serum glutamic oxaloacetic transaminase and glutamic propylic transaminase activities pre and post challenged with V. harveyi B0003 (P < 0.05). B. subtilis B0E9 and E. faecalis AT5 led to significant improvement (P < 0.05) in the serum complement 3 content (un-detected after challenged with V. harveyi B0003), lysozyme activity and skin mucosal immunity (such as IL-6, IL-10 and lysozyme expression) pre and post challenged with V. harveyi B0003, which was generally consistent with the cumulative mortality after challenged with V. harveyi B0003. This induced activations of serum and skin mucosal immunities were consistent with the microbiota data showing that B. subtilis B0E9 and E. faecalis AT5 modulated the overall structure of intestinal and skin mucosal microbiota, and in particular, the relative abundance of potentially pathogenic Achromobacter decreased while beneficial Streptococcus, Rothia, and Lactobacillus increased in fish fed with B. subtilis B0E9 and E. faecalis AT5. Overall, autochthonous B. subtilis B0E9 and E. faecalis AT5 (particularly E. faecalis AT5) can improve liver health, serum and skin immunities (especially up-regulated lysozyme activity and inflammation-related genes expression), positively shape gut and skin mucosal microbiota, and enhance red-head disease resistance of yellow drum.

Molecular Cloning and Functional Characterization of Galectin-1 in Yellow Drum (Nibea albiflora)

Galectins are proteins that are involved in the innate immune response against pathogenic microorganisms. In the present study, the gene expression pattern of galectin-1 (named as NaGal-1) and its function in mediating the defense response to bacterial attack were investigated. The tertiary structure of NaGal-1 protein consists of homodimers and each subunit has one carbohydrate recognition domain. Quantitative RT-PCR analysis indicated that NaGal-1 was ubiquitously distributed in all the detected tissues and highly expressed in the swim-bladder of Nibea albiflora, and its expression could be upregulated by the pathogenic Vibrio harveyi attack in the brain. Expression of NaGal-1 protein in HEK 293T cells was distributed in the cytoplasm as well as in the nucleus. The recombinant NaGal-1 protein by prokaryotic expression could agglutinate red blood cells from rabbit, Larimichthys crocea, and N. albiflora. The agglutination of N. albiflora red blood cells by the recombinant NaGal-1 protein was inhibited by peptidoglycan, lactose, D-galactose, and lipopolysaccharide in certain concentrations. In addition, the recombinant NaGal-1 protein agglutinated and killed some gram-negative bacteria including Edwardsiella tarda, Escherichia coli, Photobacterium phosphoreum, Aeromonas hydrophila, Pseudomonas aeruginosa, and Aeromonas veronii. These results set the stage for further studies of NaGal-1 protein in the innate immunity of N. albiflora.

Characterization of a novel Toll-like receptor 13 homologue from a marine fish Nibea albiflora, revealing its immunologic function as PRRs

Congenital immunity mediated by Toll-like receptor (TLR) family is the first line of defense for disease-resistant immunity of fish and plays a vital role as a bridge between innate immunity and acquired immunity. As a less known member of the TLR family TLR13 can participate in the immune and inflammatory reactions of the body for recognizing the conserved sequence of 23S rRNA in bacteria and induce immune response. In this study, the full-length cDNA of TLR13 from Nibea albiflora (named as NaTLR13) was cloned and was functionally characterized. It was 4210bp (GenBank accession no. MT701899) including an open reading frame (ORF) of 2886bp to encode 962 amino acids with molecular weight of 110.37 kDa and the theoretical isoelectric point of 9.08. There were several conservative structures in NaTLR13 such as 15 leucine-rich repeat sequences (LRRs), a Toll-IL-1 receptor domain (TIR), an LRR-CT terminal domain, two LRR-TYP structures and two transmembrane domains. The multiple sequence alignment and phylogenetic analysis manifested that NaTLR13 had high similarity with Larimichthys crocea and Collichthys lucidus (88.79% and 87.02%, respectively) and they fell into the same branch. The Real-time PCR showed that NaTLR13 was expressed in all selected tissues, with the highest in the spleen, followed by the liver, kidney, gill, heart and muscle. After being challenged by Vibrio alginolyticus, Vibrio parahaemolyticus or Poly (I:C), the expression of NaTLR13 increased firstly, then decreased and finally stabilized with time for its immune defense function. Subcellular localization analysis revealed that NaTLR13 was unevenly distributed in the cytoplasm with green fluorescence and MyD88 was evenly spread in the cytoplasm with red signals. When NaTLR13 and MyD88 were co-transfected, they obviously overlapped and displayed orange-yellow color, which showed that the homologous TLR13 might interact with MyD88 for NFκB signaling pathway transmission. The functional domains of NaTLR13 (named NaTLR13-TIR and NaTLR13-LRR) were expressed in E.coli BL21 (DE3) and purified by Ni-NAT Superflow Resin conforming to the expected molecular weights, and the recombinant proteins could bind to three Vibrios (V.alginolyticus, V.parahaemolyticus and Vibrio harveyi), indicating that NaTLR13 could be bounden to bacteria through its functional domain. These results suggested that NaTLR13 might play an important role in the defense of N.albiflora against bacteria or viral infection and the data would provide some information for further understanding the regulatory mechanism of the innate immune system in fish.

Sequence and functional features of a novel scavenger receptor homolog, SCARA5 from Yellow drum (Nibea albiflora)

As an important member in SR-As, member 5 (SCARA5) can swallow apoptotic cells and foreign bodies, and participate multiple signaling pathways to inhibit tumor occurrence, development growth and metastasis. To explore its immune function, SCARA5 was identified from the yellow drum (Nibea albiflora) according to its transcriptome data, and its full-length cDNA was 6968 bp (named as NaSCARA5, GenBank accession no: MW070211) encoding 497 amino acids with a calculated molecular weight of 55.12 kDa, which had the typical motifs of SR family, such as transmembrane helix region, coil region, Pfam collagens region and SR region. BLASTp and the phylogenetic relationship analysis illustrated that the sequences shared high similarity with known SCARA5 of teleosts. Quantitative real time RT-PCR analysis showed that NaSCARA5 was expressed in intestine, stomach, liver, kidney, gill, heart and spleen, with the highest in the spleen (24.42-fold compared with that in heart). After being infected with Polyinosinic:polycytidylic acid (PolyI:C), Vibrio alginolyticus and Vibrio parahaemolyticus, NaSCARA5 mRNA were up-regulated with time dependent mode in spleen, which suggested that NaSCARA5 might play an important role in the immune process of fish. The extracellular domain of NaSCARA5 was successfully expressed in BL21 (DE3), and yielded the target protein of the expected size with many active sites for their conferring protein-protein interaction functions. After being purified by Ni-NAT Superflow resin and renatured, it was found to bind all the tested bacteria (V.parahaemolyticus,V.alginolyticus and Vibrio harveyi). The eukaryotic expression vector of the NaSCARA5-EGFP fusion protein was constructed and transferred into epithelioma papulosum cyprini (EPC) cells, and it was mainly expressed on the cell membrane indicating that NaSCARA5 was a typical transmembrane protein. The aforementioned results indicated that NaSCARA5 played a significant role in the defense against pathogenic bacteria infection as PRRs, which may provide some further understandings of the regulatory mechanisms in the fish innate immune system for SR family.

Towards Understanding PRPS1 as a Molecular Player in Immune Response in Yellow Drum (Nibea albiflora)

Phosphoribosyl pyrophosphate synthetases (EC 2.7.6.1) are key enzymes in the biological synthesis of phosphoribosyl pyrophosphate and are involved in diverse developmental processes. In our previous study, the PRPS1 gene was discovered as a key disease-resistance candidate gene in yellow drum, Nibea albiflora, in response to the infection of Vibrio harveyi, through genome-wide association analysis. This study mainly focused on the characteristics and its roles in immune responses of the PRPS1 gene in yellow drum. In the present study, the NaPRPS1 gene was cloned from yellow drum, encoding a protein of 320 amino acids. Bioinformatic analysis showed that NaPRPS1 was highly conserved during evolution. Quantitative RT-PCR demonstrated that NaPRPS1 was highly expressed in the head-kidney and brain, and its transcription and translation were significantly activated by V. harveyi infection examined by RT-qPCR and immunohistochemistry analysis, respectively. Subcellular localization revealed that NaPRPS1 was localized in cytoplasm. In addition, semi-in vivo pull-down assay coupled with mass spectrometry identified myeloid differentiation factor 88 (MyD88) as an NaPRPS1-interacting patterner, and their interaction was further supported by reciprocal pull-down assay and co-immunoprecipitation. The inducible expression of MyD88 by V. harveyi suggested that the linker molecule MyD88 in innate immune response may play together with NaPRPS1 to coordinate the immune signaling in yellow drum in response to the pathogenic infection. We provide new insights into important functions of PRPS1, especially PRPS1 in the innate immunity of teleost fishes, which will benefit the development of marine fish aquaculture.

Identification, functional characterization and expression pattern of myeloid differentiation factor 88 (MyD88) in Nibea albiflora

Myeloid differentiation factor 88 (MyD88), composed of an N-terminal death domain and a C-terminal Toll/interleukin (IL)-IR homology domain, is a key connector protein in the TLR signal transduction pathway. In this study a novel isoform of MyD88 in Nibea albiflora (named as NaMyD88) was identified and functionally characterized (GenBank accession no. MN384261.1). Its complete cDNA sequence was 1672 bp and contained an open reading frame of 879 bp encoding 292 amino acid residues, which was similar to its teleost fish counterparts in the length. The theoretical molecular mass was 33.63 kDa and the isoelectric point was 5.24. BLASTp analysis suggested that the deduced amino acids sequence of NaMyD88 shared high identity to the known MyD88, for instance, 94.77% identity with Collichthys lucidus. Sequence analysis showed that NaMyD88 protein was consistent with MyD88 protein of other species at three conserved domains, N-terminal DD, short middle domain and C-terminal TIR, and the TIR domain contained three highly conserved motifs: Box1, Box2, and Box3. NaMyD88 and red fluorescent protein (Dsred) were fused and expressed in the cytoplasm of the epithelioma papulosum cyprini (EPC cells). The NaTLR9-TIR-EGFP fusion protein, which was obtained in our previous studies, showed green fluorescence and mainly distributed in the cytoplasm. After co-transfection, NaMyD88-Dsred and NaTLR9-TIR-EGFP obviously overlapped and displayed orange-yellow color. The results showed that the homologous MyD88-Dsred could interact with NaTLR9-TIR-EGFP. Based on this result pcMV-NaMyD88-TIR-Myc plasmids and the pcDNA3.1-NaTLR9-TIR-flag were constructed and co-transfected into 293T cells for the immunoprecipitation test. According to Western blot, the protein eluted by Flag-beads could be detected by anti-Flag-tag antibody and anti-Myc tag antibody respectively, while the protein without NaTLR9-TIR could not be found, which further proved that TLR and MyD88 could interact each other. The prokaryotic plasmid of MyD88-TIR domain was constructed, expressed in BL21 (DE3) and purified by Ni-NAT super flow resin conforming to the expected molecular weight of 27 kDa with the corresponding active sites for its conferring protein-protein interaction functions. Real-time fluorescence quantitative PCR showed that NaMyD88 could be expressed in intestine, stomach, liver, kidney, gill, heart and spleen, with the highest in the kidney, and it was up-regulated after being infected with Polyinosinic:polycytidylic acid - Poly (I:C) and Pseudomonas plecoglossicida, which showed that NaMyD88 was involved in the immune response of N.albiflora. These data afforded a basis for understanding the role of NaMyD88 in the TLR signaling pathway of N.albiflora.

Exploring Sexual Dimorphism in the Intestinal Microbiota of the Yellow Drum (Nibea albiflora, Sciaenidae)

Most of fish species exhibit striking sexual dimorphism, particularly during growth. There are also sexual dimorphisms of internal organs and biological functions, including those of intestinal microbiota, which likely plays a key role in growth. In this study, the growth and intestinal microbiota of the female, male, and all-female Nibea albiflora (yellow drums) were comprehensively analyzed. The caged culture female and all-female yellow drums showed higher growth rates than males. A further analysis of the intestinal microbiota showed a significant difference in diversity between females and males in the summer, whereas there were no significant differences in the diversity and richness between females and males in the winter. In contrast, a significant difference in richness was observed between all-female and male fish, regardless of the season. Although the main composition of the intestinal microbiota showed no significant sex differences, the community structure of the intestinal microbiota of yellow drums did. Furthermore, the correlations between intestinal microbial communities are likely to be influenced by sex. The ecological processes of the intestinal microbial communities of the yellow drums showed clear sexual dimorphism. Further network analysis revealed that, although the main components of the network in the intestinal microbiota of female, male, and all-female fish were similar, the network structures showed significant sex differences. The negative interactions among microbial species were the dominant relationships in the intestinal ecosystem, and Bacteroidetes, Firmicutes, and Proteobacteria were identified as the functional keystone microbes. In addition, the functional pathways in the intestinal microbiota of yellow drums showed no significant sexual or seasonal differences. Based on the findings of this study, we gain a comprehensive understanding of the interactions between sex, growth, and intestinal microbiota in yellow drums.

Molecular insights of a novel fish Toll-like receptor 9 homologue in Nibea albiflora to reveal its function as PRRs

Toll-like receptors (TLRs) are an important class of molecules involved in non-specific immunity, and they are also the bridge connecting between non-specific immunity and specific immunity. As a vital member of TLR family TLR9 can be activated by bacterial DNA and induce the production of inflammatory cytokines. In this study, a full length of TLR9 homologue of 3677 bp in Nibea albiflora (named as NaTLR9, GenBank accession no: MN125017.1) was characterized, and its ORF was 3180 bp encoding 1059 amino acid residues with a calculated molecular weight of 121.334 kDa (pI = 6.29). Several leucine-rich repeated sequences (LRR domain) and conservative TIR domain were found in NaTLR9, which was mainly expressed in dendritic cells and macrophages. The phylogenetic and synteny analysis further revealed high sequence identity of NaTLR9 with its counterparts of other teleost, confirming their correct nomenclature and conservative during evolution as an important pattern recognition receptor. The NaTLR9-TIR-pEGFP-N1 fusion protein showed green fluorescence and mainly distributed in the cytoplasm. After co-transfection of NaTLR9-TIR-pEGFP-N1 and NaMyD88-pDsRED-Monomer-N1, green fluorescence obviously overlapped with red and changed into yellowish-green, which suggested that there might be the interaction between homologous NaTLR9-TIR and MyD88. Based on this result the pCDNA3.1-NaTLR9-TIR-flag and pcMV-NaMyD88-TIR-Myc plasmids were co-transfected into 293T cells for the immunoprecipitation test. According to Western blot, TLR9 and MyD88 protein could interact with each other. Furthermore, NaTLR9 was ubiquitously expressed in all the investigated tissues, most abundantly in head kidney, followed by stomach, spleen, liver and gill, but lower in muscle. The vitro immune stimulation experiments revealed that Pseudomonas plecoglossicida and polyinosinic-polycytidylic acid [Poly (I:C)] induced higher levels of NaTLR9 mRNA expression with the peaks of 9.52 times at 2 h and 39.91 times at 24 h compared with the control group respectively. The functional domains (LRRs and TIR, named NaTLR9-TIR and NaTLR9-LRR respectively) of NaTLR9 were expressed and purified, the recombinant proteins both could bind three kinds of typical aquatic pathogenic bacteria (Vibrio. parahaemolyticus, Vibrio alginolyticus, and Vibrio harveyi), which showed that NaTLR9 could couple to bacteria by its function domains. The aforementioned results indicated that NaTLR9 played a significant role in the defense against pathogenic bacteria infection in innate immune response of sciaenidae fish, which may provide some further understandings of the regulatory mechanisms in the teleostean innate immune system.

Transcriptome and co-expression network analyses reveal the regulatory pathways and key genes associated with temperature adaptability in the yellow drum (Nibea albiflora)

The yellow drum (Nibea albiflora) is an important marine economy fish, that is widely distributed in the coastal waters of the Northwest Pacific. To understand the molecular regulatory mechanism of the yellow drum under temperature stress, transcriptome analysis was performed under five temperature conditions (10 °C, 15 °C, 20 °C, 24 °C, 28 °C) in the present study. Compared with 20 °C, 163, 401, 276, and 372 differentially expressed genes (DEGs) were obtained at 10 °C, 15 °C, 24 °C and 28 °C, respectively. Gene Ontology (GO) analysis indicated that the DEGs were mainly involved in cellular processes, metabolic processes, catalytic activity, membrane and binding. Meanwhile, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the temperature adaptive regulation of the yellow drum was mainly involved in signal transduction, metabolism, genetic information and protein processing. Weighted gene co-expression network analysis (WGCNA) showed that HMGB1, STAT4, Noct, C1q and CRT may be the key hub genes in the response of the yellow drum to temperature stress. In addition, 20 genes that may be associated with temperature stress were identified based on comparative analysis between the KEGG enrichment and the WGCNA results. Ten DEGs were selected for further validation using quantitative real-time PCR (qRT-PCR), and the results were consistent with the RNA-seq data. This study explored the transcriptional patterns of the yellow drum under temperature stress and provided fundamental information on the temperature adaptability of this species.

Characterization and functional study of a chimera galectin from yellow drum Nibea albiflora

Galectins are protein that participates in a variety of immune responses in the process of pathogenic infections. In the present study, a chimera galectin gene was screened from the transcriptome database of Nibea albiflora, which was named as YdGal-3. The results of qRT-PCR showed that the mRNA transcripts of YdGal-3 were ubiquitously distributed in all the detected tissues. After infection with Vibrio harveyi, the expression of YdGal-3 in liver, spleen, and head kidney increased significantly. Immunohistochemistry showed that YdGal-3 protein was widely expressed in the head kidney. The purified YdGal-3 protein by prokaryotic expression agglutinated red blood cells. Sugar inhibition assay showed that the agglutinating activity of YdGal-3 protein was inhibited by different sugars including lactose, D-galactose, and lipopolysaccharide. In addition, we mutated YdGal-3 His 294 into proline (P), alanine (A), glycine (G), and aspartic acid (D), it was further proved that the residue plays a key role in agglutination. YdGal-3 agglutinated some gram-negative bacteria including Pseudomonas plecoglossicida, Vibrio parahemolyticus, V. harveyi, and Aeromonas hydrophila, and exhibited antibacterial activity. These results suggested that YdGal-3 protein played an important role in the innate immunity of N. albiflora.

Label-free quantitative proteomics analysis of skin of yellow drum (Nibea albiflora) reveals immune mechanism against Cryptocaryon irritans

To explore the resistance mechanism of locally infected skin of yellow drum (Nibea albiflora) against Cryptocaryon irritans infection, N. albiflora were infected with C. irritans at a median lethal concentration of 2050 theronts/g fish. Then, the skin of the infected group (24 hT and 72 hT) and the control group (24 hC and 72 hC) were sampled at 24 h and 72 h for quantitative proteomics analysis. A total of 643 proteins were identified, of which 61 proteins were significantly affected by interaction between time and infection, 83 and 119 proteins were significantly affected by the infection and time, respectively. In addition, 17, 61, 81 and 45 differentially expressed proteins (DEPs) were obtained from pairwise comparison (24 hT vs 24 hC, 72 hT vs 72 hC, 72 hT vs 24 hT and 72 hC vs 24 hC), respectively. DEPs in 24 hT vs 24 hC and 72 hT vs 72 hC were mainly enriched in Gene Ontology terms (transferase activity, protein folding and isomerase activity) and Kyoto Encyclopedia of Genes and Genomes pathways (biosynthesis of antibiotics, carbon metabolism and Citrate cycle). Among them, enriched DEPs were malate dehydrogenase 2 (MDH2), malate dehydrogenase 1 ab (MDH 1 ab), citrate synthase, etc. Immune-related DEPs such as complement component C3 and Cell division cycle 42 were involved in response to stimulus and signal transduction, etc. Also, DEPs such as collagen, heat shock protein 75 and MDH2 play a role in helping fish skin wounds to heal and provide energy. Furthermore, protein-protein interaction analysis indicated that 18 proteins such as MDH2, MDH 1 ab, complement C3 and collagen were interrelated. In conclusion, this study found that many proteins in N. albiflora contribute to resist against C. irritans and promote fish recovery.

Physiological responses to cold and starvation stresses in the liver of yellow drum (Nibea albiflora) revealed by LC-MS metabolomics

As global climate changes, mass mortality in farmed fish associated with the severely cold weather has aroused growing concerns. Yellow drum (Nibea albiflora) is an important maricultured fish in China, whereby its aquaculture suffered from overwinter mortality associated with cold and cold-induced-fasting stresses. Here, by using LC-MS metabolomics combined with transcriptomics, we investigated the physiological responses of yellow drum liver to cold and starvation stresses. The experiment involved four groups: 16 °C fed group (CG1), 16 °C unfed group (CG2), 8 °C fed group (EG1), and 8 °C unfed group (EG2). Under cold stress, a total of 308 and 257 differential metabolites were identified in EG1 vs. CG1 and EG2 vs. CG2, respectively, showing 5 overlapping significant pathways: glutathione metabolism, biosynthesis of unsaturated fatty acids, galactose metabolism, arginine and proline metabolism, and ABC transporters. Intersection analysis identified that glutamate, oxidized glutathione (GSSG), and eicosenoic acid were the common metabolites induced by cold stress. Under starvation stress, a total of 300 and 215 differential metabolites were identified in CG2 vs. CG1 and EG2 vs. EG1, respectively, showing 2 overlapping significant pathways: glutathione metabolism and galactose metabolism. Intersection analysis revealed that glutamate and GSSG were the common metabolites caused by fasting. Under cold and starvation combined stresses, 286 differential metabolites were identified in EG2 vs. CG1, showing 7 influenced pathways: glycerophospholipid metabolism, biosynthesis of unsaturated fatty acids, glutathione metabolism, sphingolipid metabolism, glycosylphosphatidylinositol (GPI)-anchor biosynthesis, autophagy, and purine metabolism. Interestingly, the glutamate and GSSG were induced by both single and combined stresses of cold and starvation treatments. These findings suggest that glutathione metabolism and its related metabolites (glutamate and GSSG) could be potential biomarkers of cold and starvation stresses in yellow drum. Overall, the results of this study provided insights into the physiological regulation in response to cold and starvation stresses in this fish.

Transcriptomic analysis of Nibea albiflora skin in response to infection by Cryptocaryon irritans

Massive infection caused by Cryptocaryon irritans is detrimental to the development of marine aquaculture. Recently, our lab found that Nibea albiflora has low sensitivity and low mortality to C. irritans infection. The present study was designed to investigate the mechanisms of the N. albiflora response to C. irritans infection by analyzing transcriptome changes in the skin. Skin samples of control and experimental groups with C. irritans infection were collected at 24 and 72 h (24 h control, 24 h post-infection, 72 h control, and 72 h post-infection). Three parallels were set for each group and sample time, and a total of 12 skin samples were collected for sequencing. Overall, 297,489,843 valid paired-end reads and 48,817 unigenes were obtained with an overall length of 59,010,494 nt. In pairwise comparisons, changes in expression occurred in 1621 (764 upregulated and 857 downregulated), 285 (180 upregulated and 105 downregulated), 993 (489 upregulated and 504 downregulated), and 37 (8 upregulated and 29 downregulated) genes at 24 h control vs 24 h post-infection, 72 h control vs 72 h post-infection, 24 h post-infection vs 72 h post-infection, and 24 h control vs 72 h control, respectively. Gene Ontology (GO) analysis of differentially expressed genes (DEGs) indicated that the number of genes enriched in GO sub-categories were ordered 24 h control vs 24 h post-infection > 24 h post-infection vs 72 h post-infection >72 h control vs 72 h post-infection > 24 h control vs 72 h control. Further analysis showed that immune-related GO terms (including immune system process, complement activation, and humoral immunity) were significantly enriched at both 72 h control vs 72 h post-infection and 24 h post-infection vs 72 h post-infection, but no immune-related GO terms were significantly enriched in the 24 h control vs 72 h control and at 24 h control vs 24 h post-infection, indicating that C. irritans infection mainly affected the physiological metabolism of N. albiflora at an early stage (24 h), and immune-related genes play an important role at a later stage (72 h) of infection. In KEGG pathway analysis, the complement and coagulation cascade pathway are involved in early infection. Hematopoietic cell lineage, natural killer (NK) cell-mediated cytotoxicity, and the intestinal immune network for IgA production are involved in later infection. Further analysis showed that the alternative pathway of complement and coagulation cascades plays an important role in the resistance of N. albiflora to early C. irritans infection. During late infection, CD34, IgM, and IgD were significantly upregulated in the hematopoietic cell lineage pathway. CCR9 was significantly downregulated, and IGH and PIGR were significantly upregulated in the intestinal immune network for IgA production. GZMB and IGH were significantly downregulated in NK cell-mediated cytotoxicity. These findings indicate that acquired immunity at the mRNA level was initiated during later infection. In addition, the IL-17 signaling pathway was enriched by downregulated DEGs at 24 h post-infection vs 72 h post-infection, suggesting the inflammatory response at 24 h was stronger than at 72 h and the invasion of the parasite has a greater impact on the host.

Evaluation of Genomic Selection for Seven Economic Traits in Yellow Drum (Nibea albiflora)

Yellow drum (Nibea albiflora) is an important maricultural fish in China, and genetic improvement is necessary for this species. This research evaluated the application of genomic selection methods to predict the genetic values of seven economic traits for yellow drum. Using genome-wide single-nucleotide polymorphisms (SNPs), we estimated the genetic parameters for seven traits, including body length (BL), swimming bladder index (SBI), swimming bladder weight (SBW), body thickness (BT), body height (BH), body length/body height ratio (LHR), and gonad weight index (GWI). The heritability estimates ranged from 0.309 to 0.843. We evaluated the prediction performance of various statistical methods, and no one method provided the highest predictive ability for all traits. We then evaluated and compared the use of genome-wide association study (GWAS)-informative SNPs and random SNPs for prediction and found that GWAS-informative SNPs obviously increased. It only needed 5 and 100 informative SNPs for LHR and BT to achieve almost the same predictive abilities as using genome-wide SNPs, and for BL, SBI, SBW, BH, and GWI, about 1000 to 3000 informative SNPs were needed to achieve whole-genome level predictive abilities. It can be concluded from the test results that breeders can use fewer SNPs to save the breeding costs of genomic selection for some traits.

Skin metabolome reveals immune responses in yellow drum Nibea albiflora to Cryptocaryon irritans infection

The yellow drum Nibea albiflora is less susceptible to Cryptocaryon irritans infection than is the case with other marine fishes such as Larimichthys crocea, Lateolabrax japonicus, and Pagrus major. To investigate further their resistance mechanism, we infected the N. albiflora with the C. irritans at a median lethal concentration of 2050 theronts/g fish. The skins of the infected and the uninfected fishes were sampled at 24 h and 72 h followed by an extensive analysis of metabolism. The study results revealed that there were 2694 potential metabolites. At 24 h post-infection, 12 metabolites were up-regulated and 17 were down-regulated whereas at 72 h post-infection, 22 metabolites were up-regulated and 26 were down-regulated. Pathway enrichment analysis shows that the differential enriched pathways were higher at 24 h with 22 categories and 58 subcategories (49 up, 9 down) than at 72 h whereby the differential enriched pathways were 6 categories and 8 subcategories (4 up, 4 down). In addition, the principal component analysis (PCA) plot shows that at 24 h the metabolites composition of infected group were separately clustered to uninfected group while at 72 h the metabolites composition in infected group were much closer to uninfected group. This indicated that C. irritans caused strong metabolic stress on the N. albiflora at 24 h and restoration of the dysregulated metabolic state took place at 72 h of infection. Also, at 72 h post infection a total of 17 compounds were identified as potential biomarkers. Furthermore, out of 2694 primary metabolites detected, 23 metabolites could be clearly identified and semi quantified with a known identification number and assigned into 66 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Most of the enriched KEGG pathways were mainly from metabolic pathway classes, including the metabolic pathway, biosynthesis of secondary metabolites, taurine and hypotaurine metabolism, purine metabolism, linoleic acid metabolism, phenylalanine, tyrosine and tryptophan biosynthesis. Others were glyoxylate and dicarboxylate metabolism, glutathione metabolism, and alanine, aspartate, and glutamate metabolism. Moreover, out of the identified metabolites, only 6 metabolites were statistically differentially expressed, namely, L -glutamate (up-regulated) at 24 h was important for energy and precursor for other glutathiones and instruments of preventing oxidative injury; 15-hydroxy- eicosatetraenoic acid (15-HETE), (S)-(-)-2-Hydroxyisocaproic acid, and adenine (up-regulated) at 72 h were important for anti-inflammatory and immune responses during infection; others were delta-valerolactam and betaine which were down-regulated compared to uninfected group at 72 h, might be related to immure responses including stimulation of immune system such as production of antibodies. Our results therefore further advance our understanding on the immunological regulation of N. albiflora during immune response against infections as they indicated a strong relationship between skin metabolome and C. irritans infection.

Characterizations of intracellular copper/zinc superoxide dismutase from yellow drum (Nibea albiflora, Richardson 1846) and its gene expressions under the ammonia/nitrite stress

Intracellular copper/zinc superoxide dismutase (icCuZnSOD) is a member of superoxide dismutase family that is capable of catalyzing the superoxide radicals into either hydrogen peroxide (H₂O₂) or ordinary molecular oxygen (O₂). Unlike mammals, the study of icCuZnSOD in aquatic animals is still in the infancy stage. Here, we identified the cDNA of na-iccuznsod from yellow drum (Nibea albiflora, Richardson 1846) and obtained its fusion protein for the first time. The mRNA expressions of na-iccuznsod were investigated in different tissues, and the dominant distribution was found in head-kidney, followed by brain, liver, heart, and gill. The effects of ammonia-N/nitrite-N on the mRNA expressions of na-iccuznsod were investigated. Na-iccuznsod transcription levels showed a general tendency of an initial up-regulation followed by a down-regulation in liver, gill, and head-kidney when yellow drum were exposed to ammonia-N/nitrite-N at the lethal concentration 50 at 96 h post-treatment, suggesting the important role of Na-icCuZnSOD in eliminating reactive oxygen species (ROS) induced by ammonia-N/nitrite-N. In addition, the characteristics of Na-icCuZnSOD protein and its comparative analysis with Na-ecCuZnSOD were investigated. Na-icCuZnSOD protein showed high enzyme stabilities over a wide range of temperature (10 to 60 °C) and pH (4.9 to 11.0), indicating its broad in vitro applications in many industries. Furthermore, the comparative analysis of Na-icCuZnSOD and Na-ecCuZnSOD gives a new perspective for the study of their structure-function relationship. Collectively, the present study will advance our understanding of the toxicity of ammonia-N/nitrite-N on yellow drum through testing the mRNA expression of iccuznsod gene, and broaden our knowledge of the protein characteristics of icCuZnSOD from fish.

Overwinter mortality in yellow drum (Nibea albiflora): Insights from growth and immune responses to cold and starvation stress

The yellow drum (Nibea albiflora) is an economically important maricultured fish in China, but the aquaculture of this species has recently been limited by an increase in overwinter mortalities associated with cold and starvation stress due to global climate changes. To better understand the interaction between starvation and cold-stress-driven overwinter mortality, we investigated the effects of these stresses on the growth performance, liver lesions, and immune response of yellow drum fish. The fish were subjected to different cold treatments and under starvation stress. The experiment lasted 30 days and involved four experimental groups: a fed group and a fasted group maintained at 16 °C (control), and a fed group and a fasted group subjected to cold stress at 8 °C. We found that the growth of yellow drum was severely affected by cold temperatures and starvation. Throughout the experimental period, the body weights were significantly lower in the groups subjected to starvation and cold stress than in the control group. The liver cells showed irregular shapes and disorderly arrangements in the stress groups; indicating liver lesions. The gene expressions of antioxidant enzymes (copper, zinc superoxide dismutase, manganese superoxide dismutase, iron superoxide dismutase, and catalase) in the liver were lower in the groups subjected to starvation and cold stress than in the control groups. These results were basically consistent with the enzyme activities of superoxide dismutase and catalase tested in the livers. In addition, activities of immunomodulatory enzymes (alkaline phosphatase and acid phosphatase) were also inhibited in groups subjected to stress throughout the experiment period. These findings suggested that starvation and cold stress inhibited growth, depressed liver function, and suppressed the immune system of yellow drum, which likely would lead to physiological failure and increased susceptibility to infection. The present study offers insights into the physiological and immune response of yellow drum under cold and starvation stress. These insights not only provide baseline information from which effective strategies can be established and appropriate management decisions formulated, but can also be used to improve the overwinter survival of this important fish species in China.

Transcriptional response to low temperature in the yellow drum (Nibea albiflora) and identification of genes related to cold stress

The yellow drum (Nibea albiflora) is an economically important maricultured fish in China, but the aquaculture of this species is severely affected by overwinter mortality associated with cold stress. Characterization of the molecular mechanisms underlying the susceptibility of the yellow drum to cold might increase our understanding of how this fish adapts to environmental challenges. Here, the transcriptional response of the yellow drum to cold stress (7.5 °C) was investigated with RNA-Seq analysis. We compared brain and muscle transcriptomes among cold-tolerant (Tol) fish that survived the cold treatment, cold-sensitive (Sen) fish that were killed by the cold treatment, and control (Con) fish that were not subjected to cold. Our analysis recovered 233,245 unigenes. The genes (DEGs) differentially expressed in the brain and muscle of the Tol versus Con group, the Sen versus Con group, and the Tol versus Sen group had tissue-specific expression patterns. Gene ontology, enrichment, and pathway analyses indicated the most highly enriched pathways in the DEGs were signaling molecules and interaction, signal transduction, carbohydrate metabolism, lipid metabolism, digestive system, and endocrine system pathways. These pathways were all associated with biological functions relevant to cold adaptation in the yellow drum, including transduction of stress signals, energy metabolism, and stress-induced cell membrane changes. We identified genes likely to be involved in cold-susceptibility and -tolerance as those differentially expressed in the Tol group as compared to the Sen group. Further investigation and characterization of these candidate genes might improve our understanding of the mechanisms underlying cold adaptation in the yellow drum.

Comparison of the susceptibility and resistance of four marine perciform fishes to Cryptocaryon irritans infection

Cryptocaryon irritans is a type of marine ectoparasitic ciliate that infects teleost fishes. To illustrate the susceptibility and innate immune mechanism of fishes to C. irritans, four species of marine perciform fishes were selected in Fujian Province, a high-prevalence area of cryptocaryoniasis in China. The survival, diameter/number of tomonts, and infection ratio among Larimichthys crocea, Lateolabrax japonicus, Pagrus major, and Nibea albiflora were compared after artificial infection. Meanwhile, the immobilization titers of four fish species with no C. irritans infection were detected. Results showed that survival and serum immobilization titer of N. albiflora were significantly higher than those of the other three fish species. A strong negative linear correlation was found between the survival/serum immobilization titer and the mean tomont diameter. In addition, the smallest C. irritans infection ratio was found in N. albiflora, implying that the serum of fishes especially that of N. albiflora, inhibited the development of parasitic C. irritans cells, and the smallest tomont size was directly related to the number of infective theronts corresponding to the highest survival of fish. Moreover, complement activity inhibition assays suggested that the alternative complement pathway might play a major role in C. irritans resistance.

The identification of growth, immune related genes and marker discovery through transcriptome in the yellow drum (Nibea albiflora)

Yellow drum (Nibea albiflora) is a commercially important marine fish, which is widely distributed in the coastal waters of China, Japan and Korea. Wild yellow drum resources have dramatically declined due to overfishing and ocean pollution. Genetic data can contribute to biodiversity conservation and protection. And molecular markers can play important roles in genetic breeding and aid in germplasm preservation in fish. In this study, 11 tissues (brain, heart, liver, kidney, muscle, head kidney, skin, fin, spleen, gonad and air bladder) were collected for pooled RNA sequencing. The unigenes were assembled using Trinity and EvidentialGene, and were then aligned to nr, nt, Swiss-Prot GO, KEGG, and KOG for annotation. Molecular markers (e.g. simple sequence repeat, SSR and single nucleotide polymorphism, SNP) were detected using MIcroSAtellite identification tool (MISA) and Genome Analysis Tool Kit (GATK). All clean reads were assembled into 109,209 transcripts, and 31,183 unigenes were generated after pruning and classifying, ranging from 201 to 19,857 bp in length (1230 bp in average), and 26,728 (85.7%) assembled unigenes had significant hits in public databases. Total of 27 and 103 unigenes were respectively identified as involved in growth- and immune-related pathways in the N. albiflora transcriptome. In addition, we identified a considerable quantity of molecular markers, including 11,484 SSRs and 56,186 SNPs. The growth- and immune-relevant genes and the molecular markers identified here provided a meaningful reference gene set and laid a foundation for future genetic selection and breeding for this species.