The CC and CXC chemokine receptors in channel catfish (Ictalurus punctatus) and their involvement in disease and hypoxia responses

Characterization, immune response and antibacterial mechanism of CXCL12 in black rockfish (Sebastes schlegelii)

Black rockfish (Sebastes schlegelii) is one of the most important mariculture fish in the Western North Pacific. Although the crucial roles of CXCL12 in immune responses against bacterial infection are well-known, the specific mechanisms underlying its involvement in fish immunity remain poorly understood. In this study, we systematically characterized CXCL12a and CXCL12b in Sebastes schlegelii (SsCXCL12a and SsCXCL12b), Firstly, SsCXCL12a/b were ubiquitously expressed across all seven tissues. Both SsCXCL12a/b were significantly differentially expressed in gill, kidney, liver, and spleen after Aeromonas salmonicida infection. Secondly, both rSsCXCL12a/b were observed to possess chemotactic activity towards spleen and peripheral blood leukocytes. Thirdly, the pathogen binding ability of rSsCXCL12a and rSsCXCL12b might be fulfilled through the recognition of PAMPs (Pathogen-Associated Molecular Patterns) on the surface of bacteria. rSsCXCL12a/b showed local agglutination effect to different bacteria. Subsequently, by detecting the permeability of the cell membrane, it was speculated that membrane attack might be one of the mechanisms by which rSsCXCL12a/b exert antimicrobial effects. Finally, it was speculated that CXCL12a/CXCR4b and CXCL12b/CXCR4a might be the major antimicrobial axes in black rockfish using Dual-Luciferase reporter gene assay system. Overall, the CXCL12/CXCR4 axis is critically involved in the immune response of S. schlegelii against bacterial infection.

Characterization, expressional and evolutionary analysis of five fish-specific CCRs (CCR4La, CCR4Lc, CCR12a1, CCR12a2, and CCR12b) in largemouth bass (Micropterus salmoides)

CC chemokine receptors (CCRs), the numbers of the G protein-coupled receptor (GPCR) superfamily, had crucial roles in treating infection, inflammation, and tissue damage by binding to their ligands. In this study, five fish-specific CCRs, namely CCR4La, CCR4Lc, CCR12a1, CCR12a2, and CCR12b, were identified in largemouth bass (Micropterus salmoides). The correction of nomenclatures of these CCRs were confirmed by phylogenetic analysis, structural analysis and genomic synteny analysis. Following 1 × 106 CFU/mL and 1 × 107 CFU/mL Edwardsiella piscicida infection, these five CCRs were significantly induced in spleen of largemouth bass, indicating their important roles in the immune response against bacterial infection. Selection pressure analysis revealed that CCR4La, CCR4Lc, CCR12a1, and CCR12a2 underwent negative selection pressure, whereas CCR12b experienced positive selection pressure. Robust selection site detection methods identified that positive selected sites of CCR4La, CCR4Lc, CCR12a1, and CCR12a2 mainly distributed in their extracellular regions, which involved in ligand binding and pathogen interaction. Similarly, the positive selected sites of CCR12b were also located in its extracellular regions. The accuracy of the pressure selected sites were also validated by molecular docking analysis. The potential ligands for these five CCRs were identified by molecular docking analysis, with finding that CCL3 and CCL5 might be the ligands of largemouth bass CCR4La/Lc, and CCL5, CCL8, CCL7, CCL13 and CCL26 might be that of largemouth bass CCR12a1/a2/b. Our results provided basis for elucidating the functions of chemokine-receptor complex in largemouth bass.

Short time-series expression transcriptome data reveal the gene expression patterns and potential biomarkers of blood infection with LPS and poly (I:C) in Mandarin fish (Siniperca chuatsi)

Blood transcriptomics has emerged as a vital tool for tracking the immune system and supporting disease diagnosis, prognosis, treatment, and research. The present study was conducted to analyze the gene expression profile and potential biomarker candidates using the whole blood of mandarin fish (Siniperca chuatsi) infected with LPS or poly (I:C) at 0 h, 3 h, 6 h, and 12 h. Our data suggest that 310 shared differentially expressed genes (DEGs) were identified among each comparison group after LPS infection, and 137 shared DEGs were identified after poly (I:C) infection. A total of 62 shared DEGs were differentially expressed in all compared groups after LPS or poly (I:C) infection. Pathways analysis for DEGs in all different compared groups showed that cytokine-cytokine receptor interaction was the most enrichment pathway. The expression levels of genes C-X-C chemokine receptor type 2-like (cxcr2), chemokine (C-C motif) receptor 9a (ccr9a), chemokine (C-C motif) receptor 9b (ccr9b), chemokine (C-X-C motif) receptor 4b (cxcr4b), and interleukin 10 receptor alpha (il10ra) were significantly different in all compared groups and most enriched in cytokine-cytokine receptor interaction pathway. The protein-protein interactions analysis among all shared DEGs showed that cxcr4 was the hub gene with the highest degree. The biomarker candidates discovered in this study may, following validation, prove effective as diagnostic tools in monitoring mandarin fish diseases.

Evolutionary traits and functional roles of chemokines and their receptors in the male pregnancy of the Syngnathidae

Vertebrates have developed various modes of reproduction, some of which are found in Teleosts. Over 300 species of the Syngnathidae (seahorses, pipefishes and seadragons) exhibit male pregnancies; the males have specialized brood pouches that provide immune protection, nourishment, and oxygen regulation. Chemokines play a vital role at the mammalian maternal-fetal interface; however, their functions in fish reproduction are unclear. This study revealed the evolutionary traits and potential functions of chemokine genes in 22 oviparous, ovoviviparous, and viviparous fish species through comparative genomic analyses. Our results showed that chemokine gene copy numbers and evolutionary rates vary among species with different modes of reproduction. Syngnathidae lost cxcl13 and cxcr5, which are involved in key receptor-ligand pairs for lymphoid organ development. Notably, Syngnathidae have site-specific mutations in cxcl12b and ccl44, suggesting immune function during gestation. Moreover, transcriptome analysis revealed that chemokine gene expression varies among Syngnathidae species with different types of brood pouches, suggesting adaptive variations in chemokine functions among seahorses and their relatives. Furthermore, challenge experiments on seahorse brood pouches revealed a joint immune function of chemokine genes during male pregnancy. This study provides insights into the evolutionary diversity of chemokine genes associated with different reproductive modes in fish.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-023-00205-x.

Effect of Agaricus bisporus Polysaccharides (ABPs) on anti-CCV immune response of channel catfish

Herein, the effects of Agaricus bisporus Polysaccharides (ABPs) on anti-channel catfish virus (CCV) infections to promote their application in channel catfish culture were explored. Transcriptome and metabolome analyses were conducted on the spleen of a CCV-infected channel catfish model fed with or without ABPs. CCV infections upregulated many immune and apoptosis-related genes, such as IL-6, IFN-α3, IFN-γ1, IL-26, Casp3, Casp8, and IL-10, and activated specific immunity mediated by B cells. However, after adding ABPs, the expression of inflammation-related genes decreased in CCV-infected channel catfish, and the inflammatory inhibitors NLRC3 were upregulated. Meanwhile, the expression of apoptosis-related genes was reduced, indicating that ABPs can more rapidly and strongly enhance the immunity of channel catfish to resist viral infection. Moreover, the metabonomic analysis showed that channel catfish had a high energy requirement during CCV infection, and ABPs could enhance the immune function of channel catfish. In conclusion, ABPs can enhance the antiviral ability of channel catfish by enhancing immune response and regulating inflammation. Thus, these findings provided new insights into the antiviral response effects of ABPs, which might support their application in aquaculture.

Transcriptome analysis of Chinese sucker (Myxocyprinus asiaticus) head kidney and discovery of key immune-related genes to cold stress after swimming fatigue

For Chinese sucker (Myxocyprinus asiaticus), passing through a dam with fast flow and cold water are always unavoidable, and this process can cause stress, disease or even death. In this study, comparative transcriptome analysis was conducted to investigate the potential immune mechanism in head kidney of M. asiaticus with swimming fatigue stress and cold stress after fatigue. In general, a total of 181,781 unigenes were generated, and 38,545 differentially expressed genes (DEGs) were identified. In these DEGs, 22,593, 7286 and 8666 DEGs were identified among groups of fatigue vs. cold, control vs. cold, and control vs. fatigue, respectively. Enrichment analysis revealed these DEGs were involved in coagulation cascades and complement, natural killer cell mediated cytotoxicity, antigen processing and presentation, Toll-like receptor signaling pathways, and chemokine signaling pathway. Notably, immune genes including heat shock protein 4a (HSP4a), HSP70 and HSP90α genes were significantly up-regulated in fishes with cold stress after fatigue. Differently, more immune genes in control vs. cold compared with that in control vs. fatigue were significantly down-regulated expression, such as claudin-15-like, Toll-like receptor 13, antimicrobial peptide (hepcidin), immunoglobulin, CXCR4 chemokine receptor, T-cell receptor, complement factor B/C2-A3, and interleukin 8. In this study, the number of DEGs in the head kidney was less than that our previous study in the spleen, which we speculated was more sensitive to changes in water temperature than the head kidney. In summary, lots of immune-related genes in the head kidney were down-regulated under cold stress after fatigue, suggesting that M. asiaticus might have experienced severe immunosuppression in the process of passing through the dam.

Hypoxia stress induces hepatic antioxidant activity and apoptosis, but stimulates immune response and immune-related gene expression in black rockfish Sebastes schlegelii

Dissolved oxygen concentrations both in the open ocean and coast have been declining due to the interaction of global climate change and human activity. Fish have evolved different adaptative strategies to cope with possibly damage induced by hypoxic environments. Black rockfish as important economic fish widely reared in the offshore sea cage, whereas related physiological response subject to hypoxia stress remained unclear. In this study, hepatic anti-oxidant enzymes (superoxide dismutase [SOD], catalase [CAT], glutathione peroxidase [GSH-Px]), aminotransferase (AST) and alanine aminotransferase (ALT) activities, lipid peroxidation (LPO), malondialdehyde (MDA) and glutathione (GSH) content, immunological parameters and the expression of apoptosis (bax, bcl2, p53, caspase3, xiap) and immune-related genes (c3, il-1β, ccl25, saa, hap, isg15) of black rockfish were determined during hypoxia and reoxygenation to illustrate the underlying defense response mechanisms. Results showed that hypoxia stress remarkably increased hepatic LPO and MDA content, AST and ALT activity and proportion of pyknotic nucleus. Hepatic SOD, CAT and GSH-Px activity manifested similar results, whereas GSH levels significantly decreased under hypoxia stress. The apoptosis rate of hepatocyte increased during hypoxia stress and reoxygenation. Meanwhile, p53, caspase3, bax and xiap mRNAs and bax/bcl2 rations were significantly up-regulated under hypoxia stress. However, bcl2 mRNA was significantly down-regulated. Interestingly, hypoxia stress significantly increased NBT-positive cell percent, phagocytic index, respiratory burst and ACH50 activity, and lysozyme activity. The mRNA levels of c3, ilβ, ccl25, saa, hap and isg15 were significantly up-regulated in the liver, spleen and head-kidney under hypoxia stress. The above parameters recovered to normal status after reoxygenation for 24 h Thus, hypoxia stress impairs hepatic antioxidant capacity, induces oxidative damage and apoptosis via the xiap-p53-bax-bcl2 and the caspase-dependent pathways, but enhances host immunity by regulating nonspecific immune indices and related genes expression to maintain homeostasis in black rockfish. These findings will help fully understand the hypoxia tolerance mechanisms of black rockfish and provide more data for offshore open ocean farming.

Genome-wide association study of host resistance to the ectoparasite Ichthyophthirius multifiliis in the Amazon fish Colossoma macropomum

BACKGROUND

Tambaqui, Colossoma macropomum, is the most important native fish species farmed in South America, particularly in Brazil, where its production is limited in the southern and southeastern regions due to disease outbreaks caused by the parasite Ichthyophthirius multifiliis. Therefore, genome level analysis to understand the genetic architecture of the host resistance against I. multifiliis is fundamental to improve this trait in tambaqui. The objective of the present study was to map QTL (quantitative trait loci) associated with resistance to I. multifiliis in tambaqui by GWAS (genome-wide association study).

METHODS AND RESULTS

Individuals belonging to seven families, which were previously submitted to an experimental challenge to assess the natural resistance to the parasite I. multifiliis, were used for genomic analysis. A total of 7717 SNPs were identified in this population by ddRAD (double digest restriction site associated DNA). GWAS revealed four SNPs significantly associated in the LGs (linkage groups) 2, 9, 11 and 20 for the traits time of death and parasite load. The SNPs explained a low proportion of the variance to I. multifiliis resistance for time of death and parasite load (about 0.622% and 0.375%, respectively). The SNPs were close to 11 genes related to the immune system: abcf3, znf830, ccr9, gli3, ackr4, tbata, ndr2, tgfbr3, nhej1, znf644b, and cldn10a.

CONCLUSIONS

In conclusion, the resistance to I. multifiliis is probably under polygenic control in tambaqui, in which different QTLs of low variance can be involved in the immune responses against this ectoparasite.

Comparative Transcriptome Analysis of Head Kidney of Aeromonas hydrophila-infected Hypoxia-tolerant and Normal Large Yellow Croaker

The large yellow croaker (Larimichthys crocea) is one of the most economically important marine fish on the southeast coast of China and much of its yield is usually lost by hypoxia. To address this problem and lay a foundation for culturing a new strain of large yellow croaker with hypoxia tolerance, our research group screened a hypoxia-tolerant population of L. crocea. Surprisingly, we also found that hypoxia-tolerant population exhibited higher survival when infected with pathogens compared to the normal population during the farming operation. In order to understand the mechanism underlying the higher survival rate of the hypoxia-tolerant population and enrich the head kidney immune mechanism of L. crocea infected with pathogens, we compared and analyzed the head kidney transcriptome of the hypoxia-tolerant and normal individuals under Aeromonas hydrophila infection. We obtained 159.68 GB high-quality reads, of which more than 87.61% were successfully localized to the reference genome of L. crocea. KEGG analysis revealed differentially expressed genes in the signaling pathways involving immunity, cell growth and death, transport and catabolism, and metabolism. Among these, the toll-like receptor signaling pathway, Nod-like receptor signaling pathway, cytokine-cytokine receptor interaction, phagosome, apoptosis, and OXPHOS pathways were enriched in both groups after infection compared to before, and were enriched in infected tolerant individuals compared to normal individuals. In addition, we found that the expression of hif1α and its downstream genes were higher in the hypoxia-sensitive group of fish than in the normal group. In conclusion, our results showed some signaling pathways and hub genes, which may participate in A. hydrophila defense in the head kidney of two populations, and may contribute to the higher survival rate in the hypoxia-tolerant population. Overall, these findings increase our understanding of the defense mechanism within the head kidney of L. crocea under A. hydrophila infection, and suggest a preliminary hypothesis for why hypoxia-tolerant individuals may exhibit a higher survival rates after infection. Our study provides scientific evidence for the breeding of a new hypoxia-tolerant strain of L. crocea for aquaculture.

Induction of attenuated Nocardia seriolae and their use as live vaccine trials against fish nocardiosis

Nocardia seriolae, a Gram-positive facultative intercellular pathogen, has been identified as the causative agent of fish nocardiosis, causing substantial mortality and morbidity of a wide range of fish species. Looking into that fact, the effective vaccine against this pathogen is urgently needed to control the significant losses in aquaculture practices. In order to induct attenuated strains for developing the potential live vaccines, the mutagenic N. seriolae strain S-250 and U-20 were obtained from wild-type strain ZJ0503 through continuous passaging and ultraviolet (UV) irradiation, respectively. Additionally, the biological characteristic, virulence, stability, mediating immune response and supplying protective efficacy to hybrid snakehead of the S-250 and U-20 strains were determined in the present study. The results showed that U-20 strain displayed dramatic changes in morphological characteristic and significant decreased in the virulence to hybrid snakehead, while that of S-250 strain had no obvious different in comparison to ZJ0503 strain. When hybrid snakehead were intraperitoneally injected with ZJ0503, S-250 and U-20 strains at their respective sub-clinical dosage, the non-specific immunity parameters (serum LYZ, POD, ACP, AKP and SOD activities), specific antibody (IgM) titers production and immune-related genes (CC1, CC2, IL-1β, IL-8, TNFα, IFNγ, MHCIα, MHCIIα, CD4, CD8α, TCRα and TCRβ) expression were up-regulated, indicating that they were able to trigger humoral and cell-mediated immune responses. Furthermore, the protective efficacy in hybrid snakehead after vaccination with ZJ0503, S-250 and U-20 strains, in terms of relative percentage survival (RPS), were 28.85%, 56.89% and 89.65% respectively. Taken together, two attenuated N. seriolae strains S-250 and U-20 were obtained successfully and they could elicit strong immune response and supply protective efficacy to hybrid snakehead against N. seriolae, which suggested that these two attenuated strains were the potential candidates for live vaccine development to control fish nocardiosis in aquaculture.

Genetic and epigenetic regulation of growth, reproduction, disease resistance and stress responses in aquaculture

Major progress has been made with genomic and genetic studies in aquaculture in the last decade. However, research on epigenetic regulation of aquaculture traits is still at an early stage. It is apparent that most, if not all, aquaculture traits are regulated at both genetic and epigenetic levels. This paper reviews recent progress in understanding of genetic and epigenetic regulation of important aquaculture traits such as growth, reproduction, disease resistance, and stress responses. Although it is challenging to make generalized statements, DNA methylation is mostly correlated with down-regulation of gene expression, especially when at promoters and enhancers. As such, methylation of growth factors and their receptors is negatively correlated with growth; hypomethylation of genes important for stress tolerance is correlated with increased stress tolerance; hypomethylation of genes important for male or female sex differentiation leads to sex differentiation into males or females, respectively. It is apparent that environmental regulation of aquaculture traits is mediated at the level of epigenetic regulation, and such environment-induced epigenetic changes appeared to be intergenerationally inherited, but evidences for transgenerational inheritance are still limited.

CC and CXC chemokines in turbot (Scophthalmus maximus L.): Identification, evolutionary analyses, and expression profiling after Aeromonas salmonicida infection

Chemokines are a superfamily of structurally related cytokines, which exert essential roles in guiding cell migration in development, homeostasis, and immunity. CC and CXC chemokines are the two major subfamilies in teleost species. In this study, a total of seventeen CC and CXC chemokines, with inclusion of twelve CC and five CXC chemokines, were systematically identified from the turbot genome, making turbot the teleost harboring the least number of CC and CXC chemokines among all teleost species ever reported. Phylogeny, synteny, and genomic organization analyses were performed to annotate these genes, and multiple chemokine genes were identified in the turbot genome, due to the tandem duplications (CCL19 and CCL20), the whole genome duplications (CCL20, CCL25, and CXCL12), and the teleost-specific members (CCL34-36, CCL44, and CXCL18). In addition, chemokines were ubiquitously expressed in nine examined healthy tissues, with high expression levels observed in liver, gill, and spleen. Moreover, most chemokines were significantly differentially expressed in gill and spleen after Aeromonas salmonicida infection, and exhibited tissue-specific and time-dependent manner. Finally, protein-protein interaction network (PPI) analysis indicated that turbot chemokines interacted with a few immune-related genes such as interleukins, cathepsins, stats, and TLRs. These results should be valuable for comparative immunological studies and provide insights for further functional characterization of chemokines in teleost.

Recent Advances in CXCL12/CXCR4 Antagonists and Nano-Based Drug Delivery Systems for Cancer Therapy

Chemokines can induce chemotactic cell migration by interacting with G protein-coupled receptors to play a significant regulatory role in the development of cancer. CXC chemokine-12 (CXCL12) can specifically bind to CXC chemokine receptor 4 (CXCR4) and is closely associated with the progression of cancer via multiple signaling pathways. Over recent years, many CXCR4 antagonists have been tested in clinical trials; however, Plerixafor (AMD3100) is the only drug that has been approved for marketing thus far. In this review, we first summarize the mechanisms that mediate the physiological effects of the CXCL12/CXCR4 axis. Then, we describe the use of CXCL12/CXCR4 antagonists. Finally, we discuss the use of nano-based drug delivery systems that exert action on the CXCL12/CXCR4 biological axis.

Transcriptome Analysis Reveals Molecular Underpinnings of Common Carp (Cyprinus carpio) Under Hypoxia Stress

As an essential environmental factor that affects the economic benefits of aquaculture, hypoxia is one of the urgent problems to be solved in the aquaculture fish breeding industry. Common carp (Cyprinus carpio) is a critical economic fish in China, and at present, there are many breeding strains of common carp with different character advantages in China, including Hebao red carp (C. carpio var wuyuanesis) and Songpu mirror carp (C. carpio var specularis). Even if the environmental adaptation of common carp is generally strong, the genetic background of hypoxia tolerance in different strains of common carp is unclear yet. This study tested the hypoxia tolerance of Songpu minor carp, Hebao red carp, and their hybrid F1 population by an acute hypoxia treatment. Muscle and liver tissues were used for transcriptome sequencing analysis to identify the key factors for hypoxia tolerance and explore the potential genetic mechanism for breeding high hypoxia tolerance in common carp. The comparative transcriptomic analysis revealed abundant hypoxia response-related genes and their differential regulation mechanism in these two tissues of different common carp strains under acute hypoxia, including immune response, cellular stress response, HIFs (hypoxia-inducible factors), MAP kinase, iron ion binding, and heme binding. Our findings will facilitate future investigation on the hypoxia response mechanism and provide a solid theoretical basis for breeding projects in common carp.

Chronic Inflammation Modulates Opioid Receptor Gene Expression and Triggers Respiratory Burst in a Teleost Model

Stress-inducing husbandry and rearing conditions, bacterial infections or parasitic diseases may all lead to chronic inflammation. The immune response will then channel energy away from growth, reproduction and other important physiological processes, to fuel immune-related metabolic responses. The present study aims to unravel the mechanisms and contribute with new information on the molecular, cellular and humoral parameters of European seabass (Dicentrarchus labrax) undergoing chronic inflammation that can be used as health indicators for application in fish health management. European seabass individuals were intra-peritoneally injected with either Freund’s Incomplete Adjuvant (FIA) to induce inflammation or Hanks Balanced Salt Solution (HBSS) to serve as sham. Fish were sampled at 24 h, 7, 14 and 21 days post-injection and blood, plasma and head-kidney were collected. The results found were clear indicators of an inflamed peritoneal cavity and an ongoing systemic immune response that persisted for at least 21 days. Locally, inflammation was characterized by an intense recruitment of immune cells that was still evident 21 days after injection, thus illustrating the chronic character of the immune response. Cellular response was also noticed peripherally with leukocyte numbers rising in the blood of FIA-injected fish. Furthermore, the cellular-mediated respiratory burst peaked at 21 days post-FIA injection, suggesting that phagocytes were still actively fighting the phlogistic agent. Regarding the head-kidney molecular analysis, cxcr4 and il34 appear to be good markers of a chronic inflammation response due to their importance for pathways with high relevance in chronic inflammation settings. In addition, opioid receptor nopr seems to be a good marker of a chronic inflammation response due to its role in detecting noxious stimuli. The present study can serve as a baseline to assess long-term immune-related responses in future studies. For that, more research is nonetheless required to select more responsive and specific molecular markers.

Comparative Transcriptome Analysis of Spleen Reveals Potential Regulation of Genes and Immune Pathways Following Administration of Aeromonas salmonicida subsp. masoucida Vaccine in Atlantic Salmon (Salmo salar)

Aeromonas salmonicida is a global fish pathogen. Aeromonas salmonicida subsp. masoucida (ASM) is classified as atypical A. salmonicida and caused huge losses to salmonid industry in China. Hence, it is of great significance to develop ASM vaccine and explore its protection mechanism in salmonids. In this regard, we conducted RNA-seq analysis with spleen tissue of Atlantic salmon after ASM vaccination to reveal genes, their expression patterns, and pathways involved in immune protections. In our results, a total of 441.63 million clean reads were obtained, and 389.37 million reads were mapped onto the Atlantic salmon reference genome. In addition, 1125, 2126, 1098, 820, and 1351 genes were significantly up-regulated, and 747, 2626, 818, 254, and 908 genes were significantly down-regulated post-ASM vaccination at 12 h, 24 h, 1 month, 2 months, and 3 months, respectively. Subsequent pathway analysis revealed that many differentially expressed genes (DEGs) following ASM vaccination were involved in cytokine-cytokine receptor interaction (TNFRSF11b, IL-17RA, CCR9, and CXCL11), HTLV-I infection (MR1 and HTLV-1), MAPK signaling pathway (MAPK, IL8, and TNF-α-1), PI3K-Akt signaling pathway (PIK3R3, THBS4, and COL2A1), and TNF signaling pathway (PTGS2, TNFRSF21-l, and CXCL10). Finally, the results of qRT-PCR showed a significant correlation with RNA-seq results, suggesting the reliability of RNA-seq for gene expression analysis. This study provided insights into regulation of gene expression and their involved pathways in Atlantic salmon spleen in responses to vaccine, and set the foundation for further study on the vaccine protective mechanism in Atlantic salmon as well as other teleost species.

The CC and CXC chemokine receptors in turbot (Scophthalmus maximus L.) and their response to Aeromonas salmonicida infection

Chemokines are crucial regulators of cell mobilization for development, homeostasis, and immunity. Chemokines signal through binding to chemokine receptors, a superfamily of seven-transmembrane domain G-coupled receptors. In the present study, eleven CC chemokine receptors (CCRs) and seven CXC chemokine receptors (CXCRs) were identified from turbot genome. Phylogenetic and syntenic analyses were performed to annotate these genes, indicating the closest relationship between the turbot chemokine receptors and their counterparts of Japanese flounders (Paralichthys olivaceus). Evolutionary analyses revealed that the tandem duplications of CCR8 and CXCR3, the whole genome duplications of CCR6, CCR9, CCR12, and CXCR4, and the teleost-specific CCR12 led to the expansion of turbot chemokine receptors. In addition, turbot chemokine receptors were ubiquitously expressed in nine examined healthy tissues, with high expression levels observed in spleen, gill, and head kidney. Moreover, most turbot chemokine receptors were significantly differentially expressed in spleen and gill after Aeromonas salmonicida infection, and exhibited general down-regulations at early time points and then gradually up-regulated. Finally, protein-protein interaction network (PPI) analyses indicated that chemokine receptors interacted with a few immune-related genes such as interleukins, Grk genes, CD genes, etc. These results should be valuable for comparative immunological studies and provide insights for further functional characterization of chemokine receptors in turbots.

CXC chemokines and their receptors in black rockfish (Sebastes schlegelii): Characterization, evolution analyses, and expression pattern after Aeromonas salmonicida infection

Chemokines are crucial regulators of cell mobilization for development, homeostasis, and immunity. Chemokines signal through binding to chemokine receptors, a superfamily of seven-transmembrane domain G-coupled receptors. In the present study, seventeen CXC chemokine ligands (SsCXCLs) and nine CXC chemokine receptors (SsCXCRs) were systematically identified from Sebastes schlegelii genome. Phylogeny, synteny, and evolutionary analyses were performed to annotate these genes, indicating that the tandem duplications (CXCL8, CXCL11, CXCL32, CXCR2, and CXCR3), the whole genome duplications (CXCL8, CXCL12, CXCL18, and CXCR4), and the teleost-specific members (CXCL18, CXCL19, and CXCL32) led to the expansion of SsCXCLs and SsCXCRs. In addition, SsCXCLs and SsCXCRs were ubiquitously expressed in nine examined healthy tissues, with high expression levels observed in head kidney, liver, gill and spleen. Moreover, most SsCXCLs and SsCXCRs were significantly differentially expressed in head kidney, liver, and gill after Aeromonas salmonicida infection, and exhibited tissue-specific and time-dependent manner. Finally, protein-protein interaction network (PPI) analysis indicated that SsCXCLs and SsCXCRs interacted with a few immune-related genes such as interleukins, cathepsins, CD genes, and TLRs, etc. These results should be valuable for comparative immunological studies and provide insights for further functional characterization of chemokines and receptors in teleost.

Dynamic and Differential Expression of Duplicated Cxcr4/Cxcl12 Genes Facilitates Antiviral Response in Hexaploid Gibel Carp

Chemokine receptor cxcr4 and its ligand cxcl12 have evolved two paralogs in the teleost lineage. In this study, we have identified four duplicated cxcr4 and cxcl12 genes from hexaploid gibel carp, Carassius gibelio, respectively. Cgcxcr4bs and Cgcxcl12as were dynamically and differentially expressed in immune-related tissues, and significantly up-regulated in head kidney and spleen after crucian carp herpesvirus (CaHV) infection. Blocking Cxcr4/Cxcl12 axis by injecting AMD3100 brought more severe bleeding symptom and lower survival rate in CaHV-infected fish. AMD3100 treatment also suppressed the up-regulation of key antiviral genes in head kidney and spleen, and resulted in more acute replication of CaHV in vivo. Consistently, the similar suppression of up-regulated expression of key antiviral genes were also observed in CAB cells treated by AMD3100 after poly(I:C) stimulation. Finally, MAPK3 and JAK/STAT were identified as the possible pathways that CgCxcr4s and CgCxcl12s participate in to promote the antiviral response in vitro.

A hypoxia-activated antibacterial prodrug

A prodrug based on a known antibacterial compound is reported to target Staphylococcus aureus and Escherichia coli under reductive conditions. The prodrug was prepared by masking the N-terminus and side chain amines of a component lysine residue as 4-nitrobenzyl carbamates. Activation to liberate the antibacterial was demonstrated on treatment with a model reductant, tin(II) chloride. The bioactivity of 1 was confirmed in antibacterial susceptibility assays whereas prodrug 2 was inactive.

The CXC chemokines and CXC chemokine receptors in orange-spotted grouper (Epinephelus coioides) and their expression after Singapore grouper iridovirus infection

Chemokines comprise a group of small molecular weight (6-14 kDa) cytokines; chemokine receptors are a superfamily of seven transmembrane domain G-coupled receptors. Both chemokines and their receptors have important roles in immune surveillance, inflammation, and development. Recently, 9 CXC chemokine ligands (CXCLs) and 8 CXC chemokine receptors (CXCRs) were identified and cloned from orange-spotted grouper (Epinephelus coioides) and annotated by phylogenetic and syntenic analyses. We detected mRNA transcripts for CXCLs and CXCRs in healthy tissues of E. coioides. Our data show that CXCL genes are highly expressed in the spleen, kidney and liver and that CXCR genes are ubiquitously expressed, rather than being expressed only in immune organs. Analysis of gene expression after Singapore grouper iridovirus infection indicated that CXCL and CXCR genes are regulated in a gene-specific manner. CXCL8 and CXCL12a were significantly upregulated in the spleen, kidney and liver of resistant fish, indicating potential roles in immunity against the pathogen. Additionally, CXCR4a was upregulated in all three organs in resistant fish, suggesting that CXCL8 or CXCL12a may participate in the immune response via interaction with CXCR4a. In addition, the new orange-spotted grouper receptor CXCR1b was found to be upregulated in the spleen and kidney of resistant fish, indicating that this receptor plays an important role in immune responses to viral infection. These results are valuable for comparative immunological studies and provide insight into the roles of these genes in viral infection.

Divergent Expression Patterns and Function of Two cxcr4 Paralogs in Hermaphroditic Epinephelus coioides

Chemokine receptor Cxcr4 evolved two paralogs in the teleost lineage. However, cxcr4a and cxcr4b have been characterized only in a few species. In this study, we identified two cxcr4 paralogs from the orange-spotted grouper, Epinephelus coioides. The phylogenetic relationship and gene structure and synteny suggest that the duplicated cxcr4a/b should result from the teleost-specific genome duplication (Ts3R). The teleost cxcr4 gene clusters in two paralogous chromosomes exhibit a complementary gene loss/retention pattern. Ec_cxcr4a and Ec_cxcr4b show differential and biased expression patterns in grouper adult tissue, gonads, and embryos at different stages. During embryogenesis, Ec_cxcr4a/b are abundantly transcribed from the neurula stage and mainly expressed in the neural plate and sensory organs, indicating their roles in neurogenesis. Ec_Cxcr4a and Ec_Cxcr4b possess different chemotactic migratory abilities from the human SDF-1α, Ec_Cxcl12a, and Ec_Cxcl12b. Moreover, we uncovered the N-terminus and TM5 domain as the key elements for specific ligand⁻receptor recognition of Ec_Cxcr4a-Ec_Cxcl12b and Ec_Cxcr4b-Ec_Cxcl12a. Based on the biased and divergent expression patterns of Eccxcr4a/b, and specific ligand⁻receptor recognition of Ec_Cxcl12a/b⁻Ec_Cxcr4b/a, the current study provides a paradigm of sub-functionalization of two teleost paralogs after Ts3R.

A Review of Molecular Responses of Catfish to Bacterial Diseases and Abiotic Stresses

Catfish is one of the major aquaculture species in the United States. However, the catfish industry is threatened by several bacterial diseases such as enteric septicemia of catfish (ESC), columnaris disease and Aeromonas disease, as well as by abiotic stresses such as high temperature and low oxygen. Research has been conducted for several decades to understand the host responses to these diseases and abiotic stresses. With the development of sequencing technologies, and the application of genome-wide association studies in aquaculture species, significant progress has been made. This review article summarizes recent progress in understanding the molecular responses of catfish after bacterial infection and stress challenges, and in understanding of genomic and genetic basis for disease resistance and stress tolerance.

Comparative transcriptome analysis of the swimbladder reveals expression signatures in response to low oxygen stress in channel catfish, Ictalurus punctatus

Channel catfish is the leading aquaculture species in the US, and one of the reasons for its application in aquaculture is its relatively high tolerance against hypoxia. However, hypoxia can still cause huge economic losses to the catfish industry. Studies on hypoxia tolerance, therefore, are important for aquaculture. Fish swimbladder has been considered as an accessory respiration organ surrounded by a dense capillary countercurrent exchange system. In this regard, we conducted RNA-Seq analysis with swimbladder samples of catfish under hypoxic and normal conditions to determine if swimbladder was responsive to low oxygen treatment and to reveal genes, their expression patterns, and pathways involved in hypoxia responses in catfish. A total of 155 differentially expressed genes (DEGs) were identified from swimbladder of adult catfish, whereas a total of 2,127 DEGs were identified from swimbladder of fingerling catfish under hypoxic condition as compared with untreated controls. Subsequent pathway analysis revealed that many DEGs under hypoxia were involved in HIF signaling pathway ( nos2, eno2, camk2d2, prkcb, cdkn1a, eno1, and tfrc), MAPK signaling pathway (voltage-dependent calcium channel subunit genes), PI3K/Akt/mTOR signaling pathway ( itga6, g6pc, and cdkn1a), Ras signaling pathway ( efna3 and ksr2), and signaling by VEGF ( fn1, wasf3, and hspb1) in catfish swimbladder. This study provided insights into regulation of gene expression and their involved gene pathways in catfish swimbladder in response to low oxygen stresses.

Basal polarization of the immune responses to Streptococcus agalactiae susceptible and resistant tilapia (Oreochromis niloticus)

One of the highest priority areas for improvement is the development of effective strategies for decreasing disease mortality levels in aquaculture production, a better understanding of the components of the fish immune system and their functions in the context of pathogen invasion is needed. Tilapia is the most common fish in South China, and Streptococcus agalactiae has become the most serious disease problem for tilapia industry in China. Here, we profiled gene expression differences between tilapia differing in their susceptibility to S. agalactiae both basally (before infection) and at three early timepoints post-infection (5 h, 50 h, and 7 d). Between group comparisons revealed 5756 unique genes differentially expressed greater than 2-fold at one or more timepoints. And the resistant fish showed much more strong ability in pathogen recognition, antigen presentation, immune activation, while the susceptible fish showed fast activation of apoptosis. Taken together, the immune profiles expand our knowledge for molecular mechanisms for disease resistance, as well as provide solid molecular resources for further identification of the candidate markers for disease-resistant selection and evaluation of disease prevention and treatment options for tilapia industry.