Molecular cloning of Y-Box binding protein-1 from mandarin fish and its roles in stress-response and antiviral immunity

Oxygen-Sensing Protein Cysteamine Dioxygenase from Mandarin Fish Involved in the Arg/N-Degron Pathway and Siniperca chuatsi Rhabdovirus Infection

Mammalia cysteamine (2-aminoethanethiol) dioxygenase (ADO) controls the stability of the regulator of G protein signaling 4 (RGS4) through the Cys branch of the Arg/N-degron pathway, thereby affecting the response of the body to hypoxia. However, the oxygen-sensing function of ADO remains unknown in teleost fish. Mandarin fish (Siniperca chuatsi) is one of the most important freshwater economic fishes in China. As the scale of the rearing density continues to increase, hypoxia has become an important factor threatening the growth of mandarin fish. Herein, the molecular characterization, the oxygen-sensing enzyme function, and the role in virus infection of ADO from mandarin fish (scADO) were explored. Bioinformation analysis results showed that scADO had all the molecular foundations for achieving thiol dioxygenase function: three histidine residues coordinated with Fe(II), PCO/ADO domain, and a "jelly roll" β-barrel structure. The expression pattern analysis showed that scAdo was highly expressed in the immune-related tissues, liver, and kidneys and responded to hypoxia on the expression level. Protein degradation experiment results revealed that scADO could lead to the degradation of RGS4 protein through the Cys branch of the Arg/N-degron pathway. Furthermore, the expression levels of scADO responded to fish virus infection. scADO could significantly promote the replication of Siniperca chuatsi rhabdovirus, and this was associated with its thiol dioxygenase activity. These findings not only demonstrate scADO as an oxygen-sensing protein in teleost fish, but are also of considerable importance for clarifying the contribution of the mechanism of hypoxia to the outbreaks of fish viruses.

Molecular Characterization and Functional Analysis of Hypoxia-Responsive Factor Prolyl Hydroxylase Domain 2 in Mandarin Fish (Siniperca chuatsi)

With increased breeding density, the phenomenon of hypoxia gradually increases in aquaculture. Hypoxia is primarily mediated by the hypoxia-inducible factor 1 (HIF-1) signaling pathway. Prolyl hydroxylase domain proteins (PHD) are cellular oxygen-sensing molecules that regulate the stability of HIF-1α through hydroxylation. In this study, the characterization of the PHD2 from mandarin fish Siniperca chuatsi (scPHD2) and its roles in the HIF-1 signaling pathway were investigated. Bioinformation analysis showed that scPHD2 had the conserved prolyl 4-hydroxylase alpha subunit homolog domains at its C-terminal and was more closely related to other Perciformes PHD2 than other PHD2. Tissue-distribution results revealed that scphd2 gene was expressed in all tissues tested and more highly expressed in blood and liver than in other tested tissues. Dual-luciferase reporter gene and RT-qPCR assays showed that scPHD2 overexpression could significantly inhibit the HIF-1 signaling pathway. Co-immunoprecipitation analysis showed that scPHD2 could interact with scHIF-1α. Protein degradation experiment results suggested that scPHD2 could promote scHIF-1α degradation through the proteasome degradation pathway. This study advances our understanding of how the HIF-1 signaling pathway is regulated by scPHD2 and will help in understanding the molecular mechanisms underlying hypoxia adaptation in teleost fish.

Interpretation of the Genotype by Tissue Interactions of Four Genes (AFP1, CIRP, YB-1, and HMGB1) in Takifugu rubripes Under Different Low-Temperature Conditions

Background: The differential expression of the same gene in different tissues could be due to the genotype effect, tissue effect, and/or genotype × tissue interactions. However, the genetic mechanisms responsible for this differential expression have not been reported to date.

Methods: Four resistance genes to low temperature, the genes for antifreeze protein (AFP), cold induced RNA binding protein (CIRP), high mobility group protein box-1 (HMGB1), and Y-box binding protein (YB-1), were measured by PCR in the liver, spleen, kidney, brain, heart, intestine, muscle, gonad, and skin of Takifugu rubripes cultured under different temperature conditions (18, 13, 8, and 5°C). Split-split-plot analysis of variance, additive main effects and multiplicative interaction (AMMI) and genotype main effects and genotype × environment interaction (GGE) biplot analysis were used to evaluate the effects of genotype × tissue interactions on gene expression.

Results: The results of split-split-plot analysis of variance showed that water temperature has a significant effect on the expression of T. rubripes cold resistant genes, while tissue × gene interaction has a highly significant effect on it. AMMI analysis showed that the contributions of genotype, tissue, and genotype × tissue interactions to the total variation in gene expression followed two trends: 1) as temperature decreased, the gene effect increased gradually and the genotype × tissue interaction decreased gradually; 2) the gene effect at 18 and 13°C was significantly lower than that at 8 and 5°C, while the interaction at 18 and 13°C was significantly higher than that at 8 and 5°C. GGE analysis showed that: at all temperatures except 8°C, the expression rankings of all four genes were highly positively correlated in all tissues except muscle; the expression stability of the genes was the same at 18°C/13°C and at 8°C/5°C; and AFP1 showed the best expression and stability among the four genes.

Conclusion: 8°C/5°C as the suitable temperature for such experiments for T. rubripes. Among the four antifreeze genes evaluated in this study, AFP1 had the best expression and stability.

An updated review of cold shock and cold stress in fish

Temperature is critical in regulating virtually all biological functions in fish. Low temperature stress (cold shock/stress) is an often-overlooked challenge that many fish face as a result of both natural events and anthropogenic activities. In this study, we present an updated review of the cold shock literature based on a comprehensive literature search, following an initial review on the subject by M.R. Donaldson and colleagues, published in a 2008 volume of this journal. We focus on how knowledge on cold shock and fish has evolved over the past decade, describing advances in the understanding of the generalized stress response in fish under cold stress, what metrics may be used to quantify cold stress and what knowledge gaps remain to be addressed in future research. We also describe the relevance of cold shock as it pertains to environmental managers, policymakers and industry professionals, including practical applications of cold shock. Although substantial progress has been made in addressing some of the knowledge gaps identified a decade ago, other topics (e.g., population-level effects and interactions between primary, secondary and tertiary stress responses) have received little or no attention despite their significance to fish biology and thermal stress. Approaches using combinations of primary, secondary and tertiary stress responses are crucial as a research priority to better understand the mechanisms underlying cold shock responses, from short-term physiological changes to individual- and population-level effects, thereby providing researchers with better means of quantifying cold shock in laboratory and field settings.

YBX has functional roles in CpG-ODN against cold stress and bacterial infection of Misgurnus anguillicaudatus

Misgurnus anguillicaudatus (M. anguillicaudatus) is a widely cultivated fish. However, in M. anguillicaudatus breeding, the frequent cold stress during daily breeding could induce immune suppression and increase the risk of infection, causing serious economic loss. Based on existing findings, CpG Oligonucleotides (CpG-ODNs) may be an ideal protective agent for low temperature fish breeding, performing anti-infective when faced with cold stress with cold shock proteins Y box binding proteins (YBX). Although YBX has pleiotropic functions, its roles in CpG-ODNs-mediated immunity (especially under cold situations) remain largely unexplored. To clarify the relationship among them, we identified the YBX1/YBX2 in M. anguillicaudatus and analyzed using a series of bioinformatics methods. After that, we immunized the fish with 3 types of CpG-ODNs and challenged with Aeromonas hydrophila (A. hydrophila). Here we showed that the best anti-bacterial effect of CpG-B was accompanied by the significant upregulation of YBX1. And the detection of the YBX1 downstream effectors confirmed that CpG-B induced the YBX1-mediated Th1 oriented responses to A. hydrophila by regulation of the NLRP3 (Caspase-A/-B), IL-1β, IL-12 and IFN-γ. Afterwards, we found that under cold stress, CpG-B can activate the NLRP3 and NF-κB pathways through YBX1, a key mediator of anti-A. hydrophila in CpG-B immunization. In this study, we demonstrated CpG-B protection against infection in low temperature, and its interaction with YBX1, expanded the research of CpG-ODN under cold stress, and provided a new CpG-ODN application for low temperature fish farming.

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.

Development of a gene-deleted live attenuated candidate vaccine against fish virus (ISKNV) with low pathogenicity and high protection

Aquaculture provides important food, nutrition, and income sources for humans. However, aquaculture industry is seriously threatened by viral diseases. Infectious spleen and kidney necrosis virus (ISKNV) disease causes high mortality and economic losses to the fish culture industry in Asia and has been listed as a certifiable disease by the International Epizootic Office. Vaccine development is urgent to control this disease. Here, a gene-deleted live attenuated candidate vaccine (ΔORF022L) against ISKNV with low pathogenicity and high protection was developed. ΔORF022L replicated well in mandarin fish fry-1 cells and showed similar structure with wild-type ISKNV. However, the pathogenicity was significantly lower as 98% of the mandarin fish infected with ΔORF022L survived, whereas all those infected with wild-type ISKNV died. Of importance, 100% of the ΔORF022L-infected fish survived the ISKNV challenge. ΔORF022L induced anti-ISKNV specific antibody response and upregulation of immune-related genes. This work could be beneficial to the control of fish diseases.

The roles of mandarin fish STING in innate immune defense against Infectious spleen and kidney necrosis virus infections

The mandarin fish Siniperca chuatsi is a cultured freshwater fish species that is popular in China because of its high market value. With the development of high-density cultural mode in mandarin fish, viral diseases such as Infectious spleen and kidney necrosis virus (ISKNV) are becoming increasingly serious. Stimulator of interferon genes (STING) is a central component in the innate immune response to cytosolic DNA and RNA derived from different pathogens. However, the roles of STING in innate immune response of mandarin fish remain unknown. In the present study, S. chuatsi STING (scSTING)-mediated host immune response against ISKNV infection was investigated. ScSTING transcription level increased remarkably in response to ISKNV infection, LPS, PMA, or poly (I:C) stimulation in mandarin fish fry (MFF-1) cells. Immunofluorescence results showed that scSTING localized majorly in the endoplasmic reticulum. scSTING overexpression remarkably increased the expression levels of scIFN-h, scMx, scISG15, scPKR, scViperin, scIL-1β, scIL-18, and scTNF-α genes. IFN-β-luciferase report assay results showed that the relative expressions of luciferin were remarkably increased in MFF-1 cells. Site mutation of serine (S) on C-terminus of scSTING showed that both S388 and S396 were important for mediated signaling. Furthermore, scSTING overexpression inhibited ISKNV infection, and knockdown of scSTING promoted ISKNV infection, indicating that scSTING could suppress ISKNV infection in MFF-1 cells. These observations suggested that the scSTING played an important role in innate immune against ISKNV infection. Our work would help elucidate the roles of teleost fish STING in innate immunity.

Y-Box Binding Proteins in mRNP Assembly, Translation, and Stability Control

Y-box binding proteins (YB proteins) are DNA/RNA-binding proteins belonging to a large family of proteins with the cold shock domain. Functionally, these proteins are known to be the most diverse, although the literature hardly offers any molecular mechanisms governing their activities in the cell, tissue, or the whole organism. This review describes the involvement of YB proteins in RNA-dependent processes, such as mRNA packaging into mRNPs, mRNA translation, and mRNA stabilization. In addition, recent data on the structural peculiarities of YB proteins underlying their interactions with nucleic acids are discussed.