Molecular cloning and characterization of crucian carp (Carassius auratus L.) interferon regulatory factor 7

The regulatory mechanisms of IRF7 mediated by the type I IFN signalling pathway against Streptococcus iniae in yellowfin seabream, Acanthopagrus latus (Hottuyn, 1782)

Interferon regulatory factor 7 (IRF7) regulates type I interferon (IFN) genes via combining to the ISRE region in the immune response against bacteria. Streptococcus iniae is one of the dominant pathogenic bacteria of yellowfin seabream, Acanthopagrus latus. However, the regulatory mechanisms of A. latus IRF7 (AlIRF7) mediated by the type I IFN signalling pathway against S. iniae was ambiguously. In the present study, IRF7, and two IFNa3s (IFNa3 and IFNa3-like) were authenticated from A. latus. The total length of AlIRF7 cDNA is 2142 bp, containing a 1314 bp open reading frame (ORF) encoding an inferred 437 amino acids (aa). Three typical regions, a serine-rich domain (SRD), a DNA-binding domain (DBD), and an IRF association domain (IAD), are conserved in AlIRF7. Furthermore, AlIRF7 is fundamentally expressed in various kinds of organs, with high levels in the spleen and liver. Additionally, S. iniae challenge promoted AlIRF7 expression in the spleen, liver, kidney, and brain. AlIRF7 is confirmed to be located at the nucleus and cytoplasm by overexpression of AlIRF7. Moreover, truncation mutation analyses shows that the regions, -821 bp to +192 bp and -928 bp to +196 bp, were known as core promoters from AlIFNa3 and AlIFNa3-like, respectively. The point mutation analyses and electrophoretic mobile shift assay (EMSA) verified that AlIFNa3 and AlIFNa3-like transcriptions are depended on the M2/5 and M2/3/4 binding sites with AlIRF7 regulation, respectively. Additionally, an overexpression experiment showed that AlIRF7 can dramatically decrease the mRNA levels of two AlIFNa3s and interferon signalling molecules. These results suggest that two IFNa3s may mediate the regulation of AlIRF7 in the immune responses of A. latus against S. iniae infection.

Molecular, ecological, and behavioural drivers of the bat-virus relationship

Bats perform important ecological roles in our ecosystem. However, recent studies have demonstrated that bats are reservoirs of emerging viruses that have spilled over into humans and agricultural animals to cause severe disease. These viruses include Hendra and Nipah paramyxoviruses, Ebola and Marburg filoviruses, and coronaviruses that are closely related to severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and the recently emerged SARS-CoV-2. Intriguingly, bats that are naturally or experimentally infected with these viruses do not show clinical signs of disease. Here we have reviewed ecological, behavioural, and molecular factors that may influence the ability of bats to harbour viruses. We have summarized known zoonotic potential of bat-borne viruses and stress on the need for further studies to better understand the evolutionary relationship between bats and their viruses, along with discovering the intrinsic and external factors that facilitate the successful spillover of viruses from bats.

Deciphering the Fine-Tuning of the Retinoic Acid-Inducible Gene-I Pathway in Teleost Fish and Beyond

Interferons are the first lines of defense against viral pathogen invasion during the early stages of infection. Their synthesis is tightly regulated to prevent excessive immune responses and possible deleterious effects on the host organism itself. The RIG-I-like receptor signaling cascade is one of the major pathways leading to the production of interferons. This pathway amplifies danger signals and mounts an appropriate innate response but also needs to be finely regulated to allow a rapid return to immune homeostasis. Recent advances have characterized different cellular factors involved in the control of the RIG-I pathway. This has been most extensively studied in mammalian species; however, some inconsistencies remain to be resolved. The IFN system is remarkably well conserved in vertebrates and teleost fish possess all functional orthologs of mammalian RIG-I-like receptors as well as most downstream signaling molecules. Orthologs of almost all mammalian regulatory components described to date exist in teleost fish, such as the widely used zebrafish, making fish attractive and powerful models to study in detail the regulation and evolution of the RIG-I pathway.

Fundamental Characteristics of Bat Interferon Systems

Interferons are an essential component of the innate arm of the immune system and are arguably one of the most important lines of defence against viruses. The human IFN system and its functionality has already been largely characterized and studied in detail. However, the IFN systems of bats have only been marginally examined to date up until the recent developments of the Bat1k project which have now opened new opportunities in research by identifying six new bat genomes to possess novel genes that are likely associated with viral tolerance exhibited in bats. Interestingly, bats have been hypothesized to possess the ability to establish a host-virus relationship where despite being infected, they exhibit limited signs of disease and still retain the ability to transmit the disease into other susceptible hosts. Bats are one of the most abundant and widespread vertebrates on the planet and host many zoonotic viruses that are highly pathogenic to humans. Several genomics, immunological, and biological features are thought to underlie novel antiviral mechanisms of bats. This review aims to explore the bat IFN system and developments in its diverse IFN features, focusing mainly on the model species, the Australian black flying fox (Pteropus alecto), while also highlighting bat innate immunity as an exciting and fruitful area of research to understand their ability to control viral-mediated pathogenesis.

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.

Molecular characterization of yellow catfish (Pelteobagrus fulvidraco) IRF7 suggests involvement in innate immune response

Interferon regulatory factor 7 (IRF7) serves as a critical mediator in the regulation of type Ι interferon (IFN) response to invading pathogens. Here, an ortholog of IRF7 was characterized in yellow catfish (Pelteobagrus fulvidraco). The full-length cDNA of PfIRF7 consisted of 1516 bp encoding a polypeptide of 425 amino acids. PfIRF7 protein comprised a typical IRF structural architecture, including a DNA binding domain (DBD), an IRF association domain (IAD) and a serine-rich domain (SRD). PfIRF7 was expressed predominantly in the immune-related tissues and transcriptionally upregulated by PolyI:C, LPS, and Edwardsiella ictaluri. Ectopic expression of PfIRF7 led to activation of fish type I IFN promoters and induction of IFN and Vig1, thereby conferring a strong antiviral effect against spring viremia of carp virus (SVCV). Overall, the present data suggest that PfIRF7 may play an essential role in type I IFN response of yellow catfish.

Molecular ontogeny of larval immunity in European eel at increasing temperatures

Temperature is a major factor that modulates the development and reactivity of the immune system. Only limited knowledge exists regarding the immune system of the catadromous European eel, Anguilla anguilla, especially during the oceanic early life history stages. Thus, a new molecular toolbox was developed, involving tissue specific characterisation of 3 housekeeping genes, 9 genes from the innate and 3 genes from the adaptive immune system of this species. The spatial pattern of immune genes reflected their function, e.g. complement component c3 was mainly produced in liver and il10 in the head kidney. Subsequently, the ontogeny of the immune system was studied in larvae reared from hatch to first-feeding at four temperatures, spanning their thermal tolerance range (16, 18, 20, and 22 °C). Expression of some genes (c3 and igm) declined post hatch, whilst expression of most other genes (mhc2, tlr2, il1β, irf3, irf7) increased with larval age. At the optimal temperature, 18 °C, this pattern of immune-gene expression revealed an immunocompromised phase between hatch (0 dph) and teeth-development (8 dph). The expression of two of the studied genes (mhc2, lysc) was temperature dependent, leading to increased mRNA levels at 22 °C. Additionally, at the lower end of the thermal spectrum (16 °C) immune competency appeared reduced, whilst close to the upper thermal limit (22 °C) larvae showed signs of thermal stress. Thus, protection against pathogens is probably impaired at temperatures close to the critical thermal maximum (CT_max), impacting survival and productivity in hatcheries and natural recruitment.

Differential interferon system gene expression profiles in susceptible and resistant gynogenetic clones of gibel carp challenged with herpesvirus CaHV

Interferon (IFN) system plays a vital role in the first line of defense against viruses. In this study, we first identified multiple transcripts of 15 IFN system genes, including PRRs (TLR2, TLR3, RIG-I, and LGP2), PRR-mediated IFN signal pathway (MyD88, MITA, and MAVS), IFN regulatory factors (IRF1, IRF3, IRF7, and IRF9), IFNs (IFNφ1 and IFNφ3), and ISGs (Mx and viperin), and one transcript of TLR9 in de novo transcriptome assembly data of gibel carp head-kidney. Multiple nucleotide alignments and phylogenetic analysis of common region showed that the transcripts of every of the 15 IFN system genes were classified into two homologs with distinctly divergent sequences, indicating that hexaploid gibel carp may be an allopolyploid. During Carassius auratus herpesvirus (CaHV) infection, gibel carp resistant clone H significantly suppressed CaHV replication with markedly less viral loads than those in highly susceptible clone A⁺ and moderately resistant clone F. Then, qPCR analyses were performed to reveal their differential and dynamic expression changes during CaHV infection in head kidney, spleen and liver among three gibel carp gynogenetic clones. Through qPCR and hierarchical clustering analysis, 8 genes, such as RIG-Is, LGP2s, IRF1-B, IRF3s, IRF7s, IRF9-B, Mxs, and viperins, were identified as candidate resistant-related genes. They remarkably increased their expression in immune tissues of three clones after CaHV infection. Significantly, the up-regulation folds of these genes in clone A⁺, F and H were related to their resistance ability to CaHV, progressively increasing from susceptible clone to resistant clone at 1 dpi. The positive correlation to the resistance ability suggested that resistant clone H immediately triggered stronger IFN response. IFNφ3 showed a different dynamic change and was sharply induced in moderately resistant clone F at 3 dpi. The other 5 IFN system genes (TLR2, TLR3, TLR9, MyD88, and MITA) maintained a low expression level after CaHV challenge. Interestingly, the A or B copies/homologs of almost these IFN system genes exhibited differential transcript abundance in immune tissue after CaHV challenge, suggesting A or B homologs might occur dominant or biased expression of homeologs during gibel carp evolution. These data provide candidate resistant-related genes for disease-resistance breeding of gibel carp.

Identification and functional characterization of interferon regulatory factor 7 involved in activation JAK/STAT pathway in miiuy croaker

Interferon regulatory factor (IRF) family is a transcription factor family which plays an important role in the regulation of natural immunity and immune cell differentiation. IRF7 is important to regulate the response of type I interferon (IFN) to viral infection. Thus, more researches of the characteristic and functions of IRF7 should be done to get better understanding of the mechanisms underlying immune reactions. Here, the characterization of full-length cDNA of IRF7 was reported from miiuy croaker. Gene characterization analysis of mmiIRF7 showed conservative with other fish and inferred that the difference of tryptophan residues in IRF7 may occurred in the period of fish-specific genome duplication (FSGD) or earlier. Syntenic analysis of IRF7 showed that fish IRF7 had more highly conserved synteny than the higher vertebrates IRF7. Luciferase reporter assays result showed the ability of mmiIRF7 for activation of IFNα, IFNβ, IFNγ and ISRE luciferase reporter. In this study, we systematically and comprehensively analyzed evolution and function of mmiIRF7, which will provide the basis for future research on fish IRF family.

Molecular cloning and functional characterization of interferon regulatory factor 7 of the barbel chub, Squaliobarbus curriculus

The interferon regulatory factor 7 (IRF7) is a critical regulator of type-I interferon-dependent immune reaction that defense against virus. To investigate the antiviral function of IRF7 of barbel chub Squaliobarbus curriculus (ScIRF7), the cDNA of ScIRF7 was cloned and characterized. The full length cDNA of ScIRF7 was 1870 bp, consisted of 41 bp 5'-UTR, 560 bp 3'-UTR and a 1269 bp open reading frame (ORF). The ORF encoded 423 amino acids with a molecular weight of 49.426 KDa and a theoretical isoelectric point of 5.71. The putative ScIRF7 protein possesses typical domains of IRF family including a conserved N-terminal DBD-binding domain (DBD), a C-terminal IRF association domain and a serine-rich domain. In the DBD, four tryptophans were found to be highly conserved among all species, whilst in another conserved tryptophan site of mammals, the corresponding amino acids were methionine for fishes. The expression level of ScIRF7 was highest in the spleen and lowest in the liver. The expression level of IFN-β was highest in the gill and lowest in the liver. After GCRV infection, expression levels changes of ScIRF7 showed an overall tendency of firstly up-regulation and then down-regulation in the spleen and the gill; and expression levels of ScIRF7 in peripheral blood lymphocyte at 24 h post-infection was highest among all time points. In pEGFP-ScIRF7 overexpressing cells, the mRNA level of ScIRF7 was firstly up-regulation and then down-regulation; and the expression of IFN-β was significantly up-regulated at 12 h post-infection than that of control group (P < 0.05), which was significantly higher than those in pEGFP-N1 overexpressing cells. The results indicated that ScIRF7 may play a key role in immune responses of barbel chub Squaliobarbus curriculus against GCRV and may also functions in the Ctenopharyngodon idellus kidney cells.

Distinct herpesvirus resistances and immune responses of three gynogenetic clones of gibel carp revealed by comprehensive transcriptomes

Background

Gibel carp is an important aquaculture species in China, and a herpesvirus, called as Carassius auratus herpesvirus (CaHV), has hampered the aquaculture development. Diverse gynogenetic clones of gibel carp have been identified or created, and some of them have been used as aquaculture varieties, but their resistances to herpesvirus and the underlying mechanism remain unknown.

Results

To reveal their susceptibility differences, we firstly performed herpesvirus challenge experiments in three gynogenetic clones of gibel carp, including the leading variety clone A⁺, candidate variety clone F and wild clone H. Three clones showed distinct resistances to CaHV. Moreover, 8772, 8679 and 10,982 differentially expressed unigenes (DEUs) were identified from comparative transcriptomes between diseased individuals and control individuals of clone A⁺, F and H, respectively. Comprehensive analysis of the shared DEUs in all three clones displayed common defense pathways to the herpesvirus infection, activating IFN system and suppressing complements. KEGG pathway analysis of specifically changed DEUs in respective clones revealed distinct immune responses to the herpesvirus infection. The DEU numbers identified from clone H in KEGG immune-related pathways, such as “chemokine signaling pathway”, “Toll-like receptor signaling pathway” and others, were remarkably much more than those from clone A⁺ and F. Several IFN-related genes, including Mx1, viperin, PKR and others, showed higher increases in the resistant clone H than that in the others. IFNphi3, IFI44-like and Gig2 displayed the highest expression in clone F and IRF1 uniquely increased in susceptible clone A⁺. In contrast to strong immune defense in resistant clone H, susceptible clone A⁺ showed remarkable up-regulation of genes related to apoptosis or death, indicating that clone A⁺ failed to resist virus offensive and evidently induced apoptosis or death.

Conclusions

Our study is the first attempt to screen distinct resistances and immune responses of three gynogenetic gibel carp clones to herpesvirus infection by comprehensive transcriptomes. These differential DEUs, immune-related pathways and IFN system genes identified from susceptible and resistant clones will be beneficial to marker-assisted selection (MAS) breeding or molecular module-based resistance breeding in gibel carp.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3945-6) contains supplementary material, which is available to authorized users.

Expression and functional characterization of interferon regulatory factors (irf2, irf7 and irf9) in the blunt snout bream (Megalobrama amblycephala)

Interferon regulatory factors (irfs) are a family of genes that encode transcription factors with important roles in regulating the expression of Type I interferons (IFNs) and other genes associated with related pathways. irfs have multitudinous functions in growth, development and regulation of oncogenesis. In this study, three irf family members (irf2, irf7, irf9) were identified and characterized in Megalobrama amblycephala at the mRNA and amino acid levels. M. amblycephala irfs share a high sequence homology with other vertebrate irfs. Constitutive expression levels of the three genes were detected (using qPCR) in all studied tissues: low to medium in kidney, gills, heart and muscle, and high in liver, spleen, intestine and blood. qPCR was also used to analyze the dynamic expression patterns of irfs in different embryonic development stages: irf2 is not activated during the embryonic development, whereas irf9 appears to play important roles around hatching and during the larval development. Transcripts of all three studied irfs were upregulated after stimulation by Aeromonas hydrophila bacterium in liver, spleen, head kidney and trunk kidney, whereas downregulation was observed in intestine and gills. The results show that these three irfs are likely to be important factors in the blunt snout bream immune system. They also provide a foundation for studying the origin and evolution of the innate immune system in the blunt snout bream.

Cloning and expression analysis of interferon regulatory factor 7 in the Pacific cod, Gadus macrocephalus

Interferon regulatory factor 7 (IRF7) plays an important role in regulating the response of type I interferon (IFN) to viral infection. To understand the mechanisms underlying immune reactions in the Pacific cod, Gadus macrocephalus, the gene encoding G. macrocephalus IRF7 was cloned and characterized. The cDNA of G. macrocephalus IRF7 was also cloned and sequenced. A cDNA sequence of 2032 bp was assembled using polymerase chain reaction (PCR) products. It contains an open reading frame of 1323 bp in length, which encoded a 440-amino acid polypeptide that comprised a DNA-binding domain (DBD), an IRF association domain (IAD), and a serine-rich domain (SRD). In the DBD, the tryptophan cluster consisted of only four tryptophans, which is a unique characteristic in fish IRF7. The mRNA of IRF7 was detected in various tissues, including in the spleen, thymus, kidney, intestine, and gills, using relative quantification PCR (R-qPCR). Dynamic expression of IRF7 was observed in larvae throughout post-hatching (ph) development, with the highest level detected at day of ph (dph) 25. Response to immune stimulation was examined by challenging larvae with polyriboinosinic polyribocytidylic acid (pIC) to mimic viral infection and elicit an immune reaction. R-qPCR revealed that the expression of IRF7 significantly increased in pIC-treated groups relative to that in the control groups, in a time-dependent manner, with peak responses at 48 and 72 h after pIC-treatment. These results show that IRF7 is expressed in various tissues of adult fish and larvae and is sensitive to viral infection, suggesting that it plays a role in antiviral immune defense in G. macrocephalus.

Characterization of Amphioxus IFN Regulatory Factor Family Reveals an Archaic Signaling Framework for Innate Immune Response

The IFN regulatory factor (IRF) family encodes transcription factors that play important roles in immune defense, stress response, reproduction, development, and carcinogenesis. Although the origin of the IRF family has been dated back to multicellular organisms, invertebrate IRFs differ from vertebrate IRFs in genomic structure and gene synteny, and little is known about their functions. Through comparison of multiple amphioxus genomes, in this study we suggested that amphioxus contains nine IRF members, whose orthologs are supposed to be shared among three amphioxus species. As the orthologs to the vertebrate IRF1 and IRF4 subgroups, Branchiostoma belcheri tsingtauense (bbt)IRF1 and bbtIRF8 bind the IFN-stimulated response element (ISRE) and were upregulated when amphioxus intestinal cells were stimulated with poly(I:C). As amphioxus-specific IRFs, both bbtIRF3 and bbtIRF7 bind ISRE. When activated, they can be phosphorylated by bbtTBK1 and then translocate into nucleus for target gene transcription. As transcriptional repressors, bbtIRF2 and bbtIRF4 can inhibit the transcriptional activities of bbtIRF1, 3, 7, and 8 by competing for the binding of ISRE. Interestingly, amphioxus IRF2, IRF8, and Rel were identified as target genes of bbtIRF1, bbtIRF7, and bbtIRF3, respectively, suggesting a dynamic feedback regulation among amphioxus IRF and NF-κB. Collectively, to our knowledge we present for the first time an archaic IRF signaling framework in a basal chordate, shedding new insights into the origin and evolution of vertebrate IFN-based antiviral networks.

Fish viperin exerts a conserved antiviral function through RLR-triggered IFN signaling pathway

Mammalian viperin is a typical interferon (IFN)-induced antiviral protein. Fish have viperin homologs; however, little is known about the expression regulation of fish viperins. In this study, we report the expression regulation and antiviral function of a fish viperin from crucian carp Carassius auratus during IFN response. Crucian carp viperin is induced at mRNA and protein levels by fish IFNs and IFN stimuli such as poly(I:C). Consistently, this gene promoter contains multiple transcription factor binding sites including IFN-stimulated response elements (ISRE) and IFN gamma activation sequences (GAS), and is activated by two types of fish IFNs and also by the intracellular and extracellular poly(I:C). Activation of crucian carp viperin promoter by the intracellular poly(I:C) is mediated by retinoic acid-inducing gene I (RIG-I)-like receptors (RLR)-triggered IFN signaling pathway, which is further verified by the findings that each signaling molecule of RLR pathway is able to induce the expression of crucian carp viperin at mRNA and protein levels. Finally, overexpression of crucian carp viperin in cultured fish cells confers significant protection against infection of grass carp reovirus (GCRV). These data suggest that similar to mammalian homologs, crucian carp viperin exerts a conserved function through RLR-triggered IFN signaling pathway.

Developmental toxicity of 2,3,7,8-tetrachlorodibenzo-p-dioxin in artificially fertilized crucian carp (Carassius auratus) embryo

2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is a persistent bioaccumulative environmental contaminant that is an endocrine disruptor. Embryos of various fish species are responsive to TCDD and have been used as an alternative method to the acute toxicity test with juvenile and adult fish. The TCDD test has similar endpoints of developmental toxicity. However, their sensitivity and signs of TCDD-induced toxicity are different depending on fish species and its habit. Crucian carp (Carassius auratus) - the sentinel species for persistent organic pollutants and a common foodfish in China, Japan, and Korea - was used to identify the developmental toxicity of TCDD. We obtained the fertilized eggs from the artificial fertilization of crucian carp (97.45% success rate). Embryos at 3h post fertilization (hpf) were exposed to no vehicle, vehicle (dimethylsulfoxide, 0.1% v/v) or TCDD (0.128, 0.32, 0.8, 2 and 5 μg/L) for 1h and then fresh water was changed and aerated. Embryonic development and toxicity were monitored until 150 hpf. TCDD-exposed group showed no effects on embryo mortality and hatching rate from 6 to 126 hpf. On the other hand, the post-hatching mortality rate in TCDD-exposed group was increased in a dose-dependent manner, especially at high doses (0.8, 2 and 5 μg/L). The LD50 for larval mortality was calculated to 0.24 ng TCDD/g embryo. Pericardial edema was continuously observed in larvae of TCDD-exposed groups from hatching complete time (78 hpf), followed by the onset of yolk sac edema. Hemorrhage and edema showed a significant increase depending on exposure concentration and time. Expression of TCDD-related CYP1A genes was evaluated quantitatively. Embryo and larvae in TCDD-exposed groups displayed a significant increase of CYP1A gene expression. Overall, we defined TCDD-induced toxicity in artificially fertilized crucian carp embryo and these results suggest that crucian carp can be applied as an early life stage model of TCDD-induced toxicity.

IRF7 in the Australian black flying fox, Pteropus alecto: evidence for a unique expression pattern and functional conservation

As the only flying mammal, bats harbor a number of emerging and re-emerging viruses, many of which cause severe diseases in humans and other mammals yet result in no clinical symptoms in bats. As the master regulator of the interferon (IFN)-dependent immune response, IFN regulatory factor 7 (IRF7) plays a central role in innate antiviral immunity. To explore the role of bat IRF7 in the regulation of the IFN response, we performed sequence and functional analysis of IRF7 from the pteropid bat, Pteropus alecto. Our results demonstrate that bat IRF7 retains the ability to bind to MyD88 and activate the IFN response despite unique changes in the MyD88 binding domain. We also demonstrate that bat IRF7 has a unique expression pattern across both immune and non-immune related tissues and is inducible by double-strand RNA. The broad tissue distribution of IRF7 may provide bats with an enhanced ability to rapidly activate the IFN response in a wider range of tissues compared to other mammals. The importance of IRF7 in antiviral activity against the bat reovirus, Pulau virus was confirmed by siRNA knockdown of IRF7 in bat cells resulting in enhanced viral replication. Our results highlight the importance of IRF7 in innate antiviral immunity in bats.

Sequence analysis and subcellular localization of crucian carp Carassius auratus viperin

Human viperin is known as an interferon (IFN)-inducible antiviral protein and localizes to endoplasmic reticulum (ER) via its N-terminal amphipathic α-helix. Little is known about subcellular localization of fish viperin. Herein, we characterized subcellular localization of a fish viperin from crucian carp Carassius auratus. Crucian carp viperin is nearly identical to the other viperin proteins in sequence, with the exception of the first N-terminal 70 amino acids that are defined as N-terminal variable domain including an amphipathic α-helix. In addition to N-terminal variable domain, crucian carp viperin protein harbors a conserved middle radical SAM domain and a conserved C-terminal domain. Subcellular localization analyses indicate that crucian carp viperin is a cytoplasmic protein associated with ER. Sequence analyses reveal that amino acids 1-74 forms an amphipathic α-helix domain that drives ER-localization of crucian carp viperin. In addition, Coimmunoprecipitation assays show that crucian carp viperin proteins are able to self-associate. These results together indicate that similar to mammalian homologs, fish viperins likely play important roles in IFN response.

Variation in embryonic mortality and maternal transcript expression among Atlantic cod (Gadus morhua) broodstock: a functional genomics study

Early life stage mortality is an important issue for Atlantic cod aquaculture, yet the impact of the cod maternal (egg) transcriptome on egg quality and mortality during embryonic development is poorly understood. In the present work, we studied embryonic mortality and maternal transcript expression using eggs from 15 females. Total mortality at 7days post-fertilization (7 dpf, segmentation stage) was used as an indice of egg quality. A 20,000 probe (20K) microarray experiment compared the 7hours post-fertilization (7 hpf, ~2-cell stage) egg transcriptome of the two lowest quality females (>90% mortality at 7 dpf) to that of the highest quality female (~16% mortality at 7 dpf). Forty-three microarray probes were consistently differentially expressed in both low versus high quality egg comparisons (25 higher expressed in low quality eggs, and 18 higher expressed in high quality eggs). The microarray experiment also identified many immune-relevant genes [e.g. interferon (IFN) pathway genes ifngr1 and ifrd1)] that were highly expressed in eggs of all 3 females regardless of quality. Twelve of the 43 candidate egg quality-associated genes, and ifngr1, ifrd1 and irf7, were included in a qPCR study with 7 hpf eggs from all 15 females. Then, the genes that were confirmed by qPCR to be greater than 2-fold differentially expressed between 7 hpf eggs from the lowest and highest quality females (dcbld1, ddc, and acy3 more highly expressed in the 2 lowest quality females; kpna7 and hacd1 more highly expressed in the highest quality female), and the 3 IFN pathway genes, were included in a second qPCR study with unfertilized eggs. While some maternal transcripts included in these qPCR studies were associated with extremes in egg quality, there was little correlation between egg quality and gene expression when all females were considered. Both dcbld1 and ddc showed greater than 100-fold differences in transcript expression between females and were potentially influenced by family. The Atlantic cod ddc (dopa decarboxylase) complete cDNA was characterized, and has a 1461bp open reading frame encoding a 486 amino acid protein that contains all eight residues of the conserved pyridoxal 5'-phosphate binding site including the catalytic lysine. This study provides valuable new information and resources related to the Atlantic cod egg transcriptome. Some of these microarray-identified, qPCR-confirmed, Atlantic cod egg transcripts (e.g. ddc, kpna7) play important roles during embryonic development of other vertebrate species, and may have similar functions in Atlantic cod.

Cloning and expression analyses of interferon regulatory factor (IRF) 3 and 7 genes in European eel, Anguilla anguilla with the identification of genes involved in IFN production

Interferon regulatory factor (IRF) 3 and IRF7 have been identified as regulators of type I interferon (IFN) gene expression in mammals. In the present study, the two genes were cloned and characterized in the European eel, Anguilla anguilla. The full-length cDNA sequence of IRF3 and IRF7 in the European eel, named as AaIRF3 and AaIRF7 consists of 2879 and 2419 bp respectively. Multiple alignments showed that the two IRFs have a highly conserved DNA binding domain (DBD) in the N terminus, with the characteristic motif containing five tryptophan residues, which is a feature present in their mammalian homologues. But, IRF7 has only four of the five residues in other species of fish. The expression of AaIRF3 and AaIRF7 both displayed an obvious dose-dependent manner following polyinosinic:polycytidylic acid (PolyI:C) challenge. In vivo expression analysis showed that the mRNA level of AaIRF3 and AaIRF7 was significantly up-regulated in response to PolyI:C stimulation in all examined tissues/organs except in muscle, with a lower level of increase observed in response to lipopolysaccharide (LPS) challenge and Edwardsiella tarda infection, indicating that AaIRF3 and AaIRF7 may be more likely involved in antiviral immune response. In addition, some pattern recognition receptors genes related with the production of type I IFNs and those genes in response to type I IFNs were identified in the European eel genome database, indicating a relatively conserved system in the production of type I IFN and its signalling in the European eel.

Immune gene discovery in the crucian carp Carassius auratus

The crucian carp Carassius auratus (Cyprinidae) is one of the important fish species in aquaculture. Although the crucian carp has several economic benefits, their immune system and gene information have not been investigated in depth as yet. Here, we performed the transcriptome analysis of C. auratus using the pyrosequencing method and selected several immune-related genes. Of unigenes obtained in this species, we identified a number of immune system-related genes (e.g. adhesive protein, antimicrobial protein, apoptosis- and cell cycle-related protein, cellular defense effector, immune regulator, pattern recognition protein, protease, protease inhibitor, reduction/oxidation-related protein, signal transduction-related protein and stress protein) that are potentially useful for studies on fish immunity. To be of public and practical use, we designed primer pairs of each gene from the crucian carp for real-time RT-PCR application and tested the amplicon identity of entire gene sets with the total RNA sample. For comparative analysis, we measured tissue-preferential transcript profiles of selected genes. This study will be helpful to extend our knowledge on the immune system of the crucian carp in comparative aspects and to develop the crucian carp as a potential model organism for aquatic quality monitoring in fish farming.

C1q-like factor, a target of miR-430, regulates primordial germ cell development in early embryos of Carassius auratus

C1q-like is a significant maternal factor of TNF/C1q super-family, and the abundant protein has been observed in both mature eggs of Carassius auratus and Carassius auratus gibelio, but its biological function in early embryo development has remained unclear. In this study, we firstly revealed a high level of maternal C1q-like transcript existence only in mature eggs of Carassius auratus, whereas no any maternal C1q-like transcript was observed in that of Carassius auratus gibelio. During embryonic development, the C1q-like zygotic expression begins around cardiopalmus stage in embryos of both Carassius auratus and Carassius auratus gibelio. Then, we examined the biological role of C1q-like by morpholino-mediated knockdown in early embryo development. Knockdown of CaOC1q resulted in a significant reduction of primordial germ cells (PGCs) in Carassius auratus, as shown by whole mount in situ hybridization with vasa-specific RNA probe, fluorescence immunostaining of vasa protein, and GFP imaging of the GFP-nanos1-3'UTR mRNA reporter. In vitro and in vivo evidence indicated that a microRNA, miR-430 could repress the C1q-like expression and PGC development. These data suggest that C1q-like should be a direct target of miR-430 and play an essential role in PGC development of Carassius auratus.

The antiviral innate immune response in fish: evolution and conservation of the IFN system

Innate immunity constitutes the first line of the host defense after pathogen invasion. Viruses trigger the expression of interferons (IFNs). These master antiviral cytokines induce in turn a large number of interferon-stimulated genes, which possess diverse effector and regulatory functions. The IFN system is conserved in all tetrapods as well as in fishes, but not in tunicates or in the lancelet, suggesting that it originated in early vertebrates. Viral diseases are an important concern of fish aquaculture, which is why fish viruses and antiviral responses have been studied mostly in species of commercial value, such as salmonids. More recently, there has been an interest in the use of more tractable model fish species, notably the zebrafish. Progress in genomics now makes it possible to get a relatively complete image of the genes involved in innate antiviral responses in fish. In this review, by comparing the IFN system between teleosts and mammals, we will focus on its evolution in vertebrates.

Association between SNPs in interferon regulatory factor 2 (IRF-2) gene and resistance to Aeromonas hydrophila in freshwater mussel Hyriopsis cumingii

Interferon regulatory factor 2 (IRF-2) is a multi-functional transcription factor in the IRF family exhibiting both transcriptional activating and repressing activities. In this study, an IRF-2 gene (HcIRF-2) from Hyriopsis cumingii was identified and characterized. The cDNA sequence consisted of 2688 bp, encoding a 329 amino acid-protein. The amino acid sequence had a highly conserved N-terminal DBD structure, containing characteristic repeats of six tryptophan residues. The 5'-flanking region contained several transcription regulation elements such as AP1, CdxA, HSF, NIT2 and HNF-3b. Nine SNPs were obtained through direct sequencing of HcIRF-2 from resistant and susceptible stock. Only +2365T/C SNP was significantly associated with resistance/susceptibility of H. cumingii to Aeromonas hydrophila both in genotype (P = 0.021) and allele (P = 0.006) analysis. The SNPs +2248T/C and +2365T/C were in high linkage disequilibrium, and haplotype analysis revealed that haplotype TT frequency in the resistant group was significantly higher than in the susceptible group. The mortality in +2248CC genotype individuals was significantly higher than in CT and TT genotype individuals. These results indicated that haplotype TT and genotype +2248CT and +2248GT individuals were resistant to A. hydrophila, which could make them potential markers in selective breeding of H. cumingii.

Advances in research of fish immune-relevant genes: a comparative overview of innate and adaptive immunity in teleosts

Fish is considered to be an important model in comparative immunology studies because it is a representative population of lower vertebrates serving as an essential link to early vertebrate evolution. Fish immune-relevant genes have received considerable attention due to its role in improving understanding of both fish immunology and the evolution of immune systems. In this review, we discuss the current understanding of teleost immune-relevant genes for both innate and adaptive immunity, including pattern recognition receptors, antimicrobial peptides, complement molecules, lectins, interferons and signaling factors, inflammatory cytokines, chemokines, adaptive immunity relevant cytokines and negative regulators, major histocompatibility complexes, immunoglobulins, and costimulatory molecules. The implications of these factors on the evolutionary history of immune systems were discussed and a perspective outline of innate and adaptive immunity of teleost fish was described. This review may provide clues on the evolution of the essential defense system in vertebrates.

Molecular regulation of interferon antiviral response in fish

Interferon (IFN) response is the first line of host defense against virus infection. The recent years have witnessed tremendous progress in understanding of fish IFN antiviral response. Varied number of IFN genes has been identified in different fish species but obviously, they do not show a one-to-one orthologous relationship with mammalian IFN homologs. These genes are divided into two groups with different abilities to induce downstream gene expression through binding to different receptor complexes. Consistently, some fish IFN-stimulated genes such as Mx and PKR have been confirmed for their antiviral effects. In this review, we focus on how fish cells respond to IFNs and how fish IFNs are triggered through TLR pathway and RLR pathway. We highlight the roles of IRF3 and IRF7 in activation of fish IFN response. In addition, the unique mechanisms underlying IRF3/7-dependent fish IFN response and auto-regulation of fish IFN gene expression are discussed.

Dynamic expression profiles of virus-responsive and putative antimicrobial peptide-encoding transcripts during Atlantic cod (Gadus morhua) embryonic and early larval development

Early life stage mortality is one of the problems faced by Atlantic cod aquaculture. However, our understanding of immunity in early life stage fish is still incomplete, and the information available is restricted to a few species. In the present work we investigated the expression of immune-relevant transcripts in Atlantic cod during early development. The transcripts subjected to QPCR analysis in the present study were previously identified as putative anti-viral or anti-bacterial genes in Atlantic cod using suppression subtractive hybridization (SSH) libraries, QPCR, and/or microarrays. Of the 11 genes involved in this study, only atf3, cxc chemokine and gaduscidin-1 were not detected at the transcript level in all developmental stages investigated from unfertilized egg to early larval stage. Adam22, hamp, il8, irf1, irf7, lgp2, sacsin, and stat1 transcripts were detected in unfertilized egg and 7h post-fertilization (~2-cell stage) embryos, showing maternal contribution of these immune-relevant transcripts to the early embryonic transcriptome. The Atlantic cod genes included in this study presented diverse transcript expression profiles throughout embryonic and early larval development. For example, adam22 and sacsin transcripts rose abruptly during blastula/gastrula stage and were then expressed at relatively high levels through subsequent embryonic and early larval developmental stages. A peak in irf1 and irf7 transcript expression during early segmentation suggests that these interferon pathway genes play developmental stage-specific roles during cod embryogenesis. Stat1 had increasing transcript expression throughout blastula/gastrula, segmentation, and early larval developmental stages. Atf3, cxc chemokine, gaduscidin-1, and il8 transcripts rose approximately 2-3 fold during hatching, supporting the hypothesis that there is preparation at the immune-relevant transcript expression level to deal with environmental pathogens that may be encountered during early larval development. The specific roles that interferon pathway and other immune-relevant genes play in early life stage cod, and the potential impact of their dynamic transcript expression on immune competence of Atlantic cod embryos and larvae, remain unclear and warrant further study.

Subcellular localization and functional characterization of a fish IRF9 from crucian carp Carassius auratus

Mammalian interferon (IFN) regulatory factor 9 (IRF-9) has long been recognized as the DNA sequence recognition subunit of IFN-stimulated gene factor 3 (ISGF3) complex, which is critical for type I IFN to induce the expression of IFN-stimulated genes (ISGs) against viral infection. Recent studies have shown that fish IFN exerts antiviral effects by induction of a number of ISGs and also of itself; however, little is known about the role of fish IRF9 in IFN signaling. Here we identify a fish IRF9 orthologue (CaIRF9) from IFN-producing cell line, crucian carp Carassius auratus blastulae embryonic (CAB) cells. Analysis of subcellular distribution of CaIRF9-green fluorescent protein indicates that CaIRF9 is constitutively present in the nucleus, which is driven by two nuclear localization signals (NLS), one locating within DNA-binding domain (DBD) of CaIRF9 and the other immediately behind DBD, although human IRF9 contains only one NLS analogous to the former of CaIRF9. Overexpression of CaIRF9 together with CaSTAT2 not only activates ISRE-containing promoter but also upregulates the expression of fish ISGs. Strikingly, CaIRF9 together with CaSTAT2 also exhibits an ability to activate crucian carp IFN promoter, and blockade of cellular CaIRF9 attenuates IFN itself-induced activation of crucian carp IFN promoter. Taken together, these data suggest that crucian carp IFN induces the expression of ISGs and also of itself possibly by the JAK-STAT signaling pathway that is conserved from fish to mammals.

Molecular characterization and transcription regulation analysis of type I IFN gene in grass carp (Ctenopharyngodon idella)

Type I interferons and interferon regulatory factor 7 (IRF7), which are crucial for innate immunity against viral infection, have been identified in many teleost fishes in recent years. In this study, the complete genomic sequence of grass carp (Ctenopharyngodon idella) type I interferon (termed CiIFN) (GU139255) and the full-length IRF7 cDNA sequence of grass carp (termed CiIRF7) (GQ141741) were cloned and characterized. CiIFN consists of 3368 bp, retaining the characteristic 5-exon/4-intron gene organization in fish type I IFNs. The CiIFN spans 5 exons and encodes a polypeptide of 180 amino acids, with the first 22 amino acids representing a putative signal peptide. The CiIFN promoter sequence was found to be 760 bp, which can be divided into a proximal region (from -1 to -140 bp) and a distal region (from -400 to -700 bp). The cDNA of CiIRF7 was found to be 1808 bp in full length, with an ORF of 1293 bp that encodes a putative protein of 430 amino acids. The putative amino acid sequence of CiIRF7 possesses a DNA-binding domain (DBD) in the N-terminal region. Real-time PCR analysis revealed that CiIFN displayed a low constitutive expression in all the tissues tested. After stimulation by polyinosinic:polycytidylic acid (Poly I:C), the expression of CiIFN was significantly up-regulated in most tissues of grass carp, with a relatively strong expression in spleen, kidney and intestine. The recombinant polypeptides of CiIRF7 and CiIRF7-nDBD were analyzed in gel mobility shift assays, along with the PCR amplification products of the proximal region (CiIFNP2), the distal region (CiIFNP6) and the full-length (CiIFNP7) of CiIFN promoter sequence. The results revealed that CiIRF7 could bind to the distal region as well as to the proximal region of CiIFN promoter sequence in vitro. Subsequently, the CiIFNPs (CiIFNP7/2/6) were cloned into pGL3-Basic vectors and CiIRF7 was subcloned into pcDNA3.1 vectors, then pGL3-CiIFNPs were separately transiently transfected or co-transfected with pcDNA3.1-CiIRF7 into the mouse myeloma cell lines (MMCL) SP2/0 and the grass carp kidney cell lines (CIK), and the impact of CiIRF7 on CiIFN promoter activity was measured by luciferase assays in the transfected cells. These results demonstrated that CiIRF7 acted as a positive regulator on the transcription of CiIFN.

Cloning and expression analysis of interferon regulatory factor (IRF) 3 and 7 in large yellow croaker, Larimichthys crocea

The interferon regulatory factor (IRF)3 and IRF7 are considered to play essential roles in innate immune system's antiviral responses. In this report, the full-length cDNA and genomic structure and immune response characterizations of IRF3 and IRF7 were investigated in large yellow croaker, Larimichthys crocea. The full-length cDNA of L. crocea (Lc)IRF3 was of 2204 bp, including a 5'-terminal untranslated region (UTR) of 41 bp, a 3'-terminal UTR of 774 bp and an open reading frame (ORF) of 1389 bp encoding a polypeptide of 462 amino acids residues. The full-length cDNA of LcIRF7 was of 1979 bp, including a 5'-terminal UTR of 47 bp, a 3'-terminal UTR of 636 bp and an ORF of 1296 bp encoding a polypeptide of 431 amino acids. The putative amino acid sequence of both LcIRF3 and LcIRF7 contained a typical IRF domain at the N-terminal and an IRF3 domain at the C-terminal. Furthermore, we obtained 4517 nucleotides (nt) LcIRF3 genome sequence based on the full-length cDNA, which contained 11 exons and 10 introns. The full-length genome sequence of LcIRF7 was of 3991 nucleotides, including 9 exons and 8 introns. Quantitative real-time reverse transcription PCR analysis revealed a broad expression of LcIRF3 and LcIRF7 with the most predominant expression of LcIRF3 and LcIRF7 in the liver and in the gill, respectively. The expression levels of LcIRF3 and LcIRF7 after challenged with LPS, poly I:C and Vibrio parahaemolyticus were tested in blood, spleen and liver. The results showed that the highest relative expression of LcIRF3 was in the liver at 24 h after poly I:C injection with 90 times greater than that of the non-injection group (p < 0.05). Moreover, LcIRF3 transcription increased significantly at most time point in blood and spleen tissue after poly I:C stimulation compared with that of the control group. After LPS injection, the peak value of LcIRF7 was in the liver with 207 times (at 3 h) as much as that in the control group (p < 0.05). In addition, LcIRF7 expression was significantly induced by poly I:C injection in spleen. Both LcIRF3 and LcIRF7 transcripts did not show significant change after V. parahaemolyticus stimulation. These results indicated that IRF3 and IRF7 might play an important role in large yellow croaker's defense against viral and bacterial infection.

Molecular characterization and expression analysis of interferon regulatory factor 5 (IRF-5) in turbot, Scophthalmus maximus

Interferon regulatory factor 5 (IRF-5) plays a role both in the antiviral and inflammatory responses. In this study, we described the structure, mRNA tissue distribution and regulation of an IRF-5 gene from turbot, Scophthalmus maximus (SmIRF-5). The gene sequence of SmIRF-5 is 4275 bp long, composed of 9 exons and 8 introns similar to known IRF-5 genes of vertebrates, and encodes a peptide of 487 amino acids. The deduced protein sequence shares the highest identity of ∼60-70% with fish IRF-5 and possesses a DNA-binding domain (DBD), a middle region (MR), an IRF association domain (IAD) and a virus activated domain (VAD) known to be important for the functions of IRF-5 in mammals. Phylogenetic analysis grouped SmIRF-5 with other IRF-5s of vertebrates. SmIRF-5 transcripts were detectable in a wide range of tissue types of healthy fish with higher levels observed in the head kidney, kidney and spleen. The SmIRF-5 was transcriptionally up-regulated by turbot reddish body iridovirus (TRBIV) but not by polyinosinic:polycytidylic acid (poly I:C) in the gills, head kidney, spleen and muscle. Both the highest inducibility and earliest induction of SmIRF-5 expression were observed in the spleen where it reached a maximum level at day 1 after infection, prior to that of turbot Mx. These findings may help to better understand the roles of SmIRF-5 in antiviral response.

Molecular cloning and characterization of interferon regulatory factor 1 (IRF-1), IRF-2 and IRF-5 in the chondrostean paddlefish Polyodon spathula and their phylogenetic importance in the Osteichthyes

The interferon regulatory factor (IRF) with its 10 members is a very important gene family related to innate immunity. Currently, most fish IRFs reported are from bony fish (teleosts). Cloning and sequencing of IRFs from chondrosteans, the so-called "ancient fish" including sturgeon, paddlefish, bichir and gar, are absent from the literature. In this study, three IRF genes PsIRF-1, PsIRF-2 and PsIRF-5, were cloned and characterized from the paddlefish (Polyodon spathula). PsIRF-1 includes an open reading frame (ORF) of 972 bp that encodes a putative protein of 324 amino acids; PsIRF-2 includes an ORF of 1023 bp encoding 341 amino acids and PsIRF-5 includes an ORF of 1491 bp that encodes 497 amino acids. The PsIRF-5 gene structure is similar to those in mammals but differs from those in teleosts in the first and second exons. Phylogenetic studies of the putative amino acid sequences of PsIRF-1, PsIRF-2 and PsIRF-5 based on the neighbor-joining and Bayesian inference method for Osteichthyes found widely accepted inter-relationships among actinopterygians and tetrapods. Reverse Transcription Polymerase Chain Reaction (RT-PCR) analysis of PsIRF-1, PsIRF-2 and PsIRF-5 in different paddlefish tissues shows higher levels of expression in gill, spleen and head kidney. Poly (I: C) (polyinosinic-polycytidylic acid) stimulation in vivo up-regulated PsIRF-1 and PsIRF-2 expression, while PsIRF-5 gene expression did not respond to the challenge of Poly (I: C).

Teleost fish interferons and their role in immunity

Interferons (IFNs) are the hallmark of the vertebrate antiviral system. Two of the three IFN families identified in higher vertebrates are now known to be important for antiviral defence in teleost fish. Based on the cysteine patterns, the fish type I IFN family can be divided into two subfamilies, which possibly interact with distinct receptors for signalling. The fish type II IFN family consists of two members, IFN-γ with similar functions to mammalian IFN-γ and a teleost specific IFN-γ related (IFN-γrel) molecule whose functions are not fully elucidated. These two type II IFNs also appear to bind to distinct receptors to exert their functions. It has become clear that fish IFN responses are mediated by the host pattern recognition receptors and an array of transcription factors including the IFN regulatory factors, the Jak/Stat proteins and the suppressor of cytokine signalling (SOCS) molecules.

Early antiviral response and virus-induced genes in fish

In fish as in mammals, virus infections induce changes in the expression of many host genes. Studies conducted during the last fifteen years revealed a major contribution of the interferon system in fish antiviral response. This review describes the screening methods applied to compare the impact of virus infections on the transcriptome in different fish species. These approaches identified a "core" set of genes that are strongly induced in most viral infections. The "core" interferon-induced genes (ISGs) are generally conserved in vertebrates, some of them inhibiting a wide range of viruses in mammals. A selection of ISGs -PKR, vig-1/viperin, Mx, ISG15 and finTRIMs - is further analyzed here to illustrate the diversity and complexity of the mechanisms involved in establishing an antiviral state. Most of the ISG-based pathways remain to be directly determined in fish. Fish ISGs are often duplicated and the functional specialization of multigenic families will be of particular interest for future studies.

Cloning and expression analysis of interferon regulatory factor 7 (IRF-7) in turbot, Scophthalmus maximus

Interferon regulatory factor (IRF) 7 is known as the master regulator of type I interferon (IFN)-dependent immune responses in mammals. In this study, the cDNA and genomic sequences of turbot (Scophthalmus maximus) IRF-7 (SmIRF-7) were cloned and found to encode a putative protein of 439 amino acids. The gene is composed of 10 exons and 9 introns similar to known IRF-7 genes of fish. The SmIRF-7 shows the highest amino acid identity of 49.0-80.3% to fish IRF-7 and possesses a DNA-binding domain (DBD), an IRF association domain (IAD) and a serine-rich domain (SRD) of vertebrate IRF-7. In addition, the tryptophan cluster of SmIRF-7 DBD consists of only four tryptophans, which is a characteristic unique to all fish IRF-7 members. The SmIRF-7 transcripts were expressed constitutively in all analyzed tissues of healthy turbot, with higher levels observed in immune relevant tissues. Gene expressions of SmIRF-7 and Mx were monitored over a 7-day time course by quantitative real time PCR in head kidney and muscle of turbot challenged with turbot reddish body iridovirus (TRBIV), which is a prevalent viral pathogens in farmed turbot in China. Both genes were up-regulated by TRBIV although their inducibility was much weaker in the muscle. The peak levels of SmIRF-7 transcripts were detected at day 2 post-infection in the two organs with a 12- and 4.5-fold increase, respectively. Further, the Mx showed two waves of induced expression and the maximum expression of SmIRF-7 arose earlier than the second wave of the Mx expression in both organs. These findings contribute to an understanding of functions of SmIRF-7 in antiviral response.

Molecular Cloning and Characterization of the Estrogen Receptor from the Striped Bitterling (Acheilognathus yamatsutae)

OBJECTIVES

In order to identify the possibility of striped bitterling (SB) (Acheilognathus yamatsutae) being used as a test species for estrogenic endocrine disrupting chemicals (EEDCs), we carried out the cloning and sequence characterization of the estrogen receptor (ER).

METHODS

The ER from a striped bitterling was obtained by reverse transcriptase-polymerase chain reaction (RT-PCR), 5'- and 3'-rapid amplification of cDNA ends (5'-RACE and 3'-RACE) and T-vector cloning. The expression of ER mRNA was also analyzed in six tissues (brain, liver, kidney, gill, gonad, and intestines) by real-time PCR.

RESULTS

We obtained an ER from the striped bitterling. The SB ER cDNA was 2189 base pairs (bp) in length and contained a 1707 bp open reading frame that encoded 568 amino acid residues. The SB ER amino acid sequence clustered in a monophyletic group with the ERα of other fish, and was more closely related to zebrafish ERα (88% identity) than to the ERα of other fish. The SB ER cDNA was divided into A/B, C, D, E and F domains. The SB ER has conserved important sequences for ER functions, such as the DNA binding domain (D domain), which are consistent with those of other teleosts.

CONCLUSIONS

The ER of the striped bitterling could provide basic information in toxicological studies of EEDCs in the striped bitterling.

Interferon regulatory factor 3 (IRF-3) in Japanese flounder, Paralichthys olivaceus: sequencing, limited tissue distribution, inducible expression and induction of fish type I interferon promoter

Two cDNAs with different 3'-untranslated region (UTR) encoding an interferon regulatory factor 3 (IRF-3) were cloned from head kidney of Japanese flounder, Paralichthys olivaceus, by reverse transcription polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE) methods. Sequence analysis reveals that they were generated by alternative polyadenylation. The predicted protein consists of 467 amino acid residues which shares the highest identity of 50.7-57.6% to fish IRF-3 and possesses a DNA-binding domain (DBD), an IRF association domain (IAD) and a serine-rich domain (SRD) of vertebrate IRF-3. The presence of these domains along with phylogenetic analysis places it into the IRF-3 group of the IRF-3 subfamily. RT-PCR analysis revealed that flounder IRF-3 was expressed constitutively in limited tissue types including head kidney, spleen, kidney, heart, gill, intestine and liver. A quantitative real time PCR assay was employed to monitor expression of IRF-3, type I interferon (IFN) and Mx in flounder head kidney and gill. All three genes were up-regulated by polyinosinic:polycytidylic acid (polyI:C) and lymphocystis disease virus (LCDV) with an earlier but slight and less persistent increase in transcription levels seen for the IRF-3. Finally, flounder IRF-3 was proved to induce fish type I IFN promoter in FG9307 cells, a flounder gill cell line, by a luciferase assay. These results provide insights into the roles of fish IRF-3 in the antiviral immunity.

Characterization of fish IRF3 as an IFN-inducible protein reveals evolving regulation of IFN response in vertebrates

In mammals, IFN regulatory factor (IRF) 3 is a critical player in modulating transcription of type I IFN and IFN-stimulated genes (ISGs). In this study, we describe the roles of crucian carp (Carassius auratus L.) IRF3 in activating fish IFN and ISGs. Fish IRF3 exhibits a large sequence divergence from mammalian orthologs. Whereas mammalian IRF3 is constitutively expressed, fish IRF3 protein is significantly upregulated by IFN, poly-IC, and other stimuli known as IFN inducers in mammals. The IFN-inducible property of fish IRF3 is consistent with the comparative analysis of 5' flanking regulatory region of vertebrate IRF3 genes, which reveals the presence of typical IFN-stimulated response elements in fish and amphibians, but an absence in tetrapods. Furthermore, either IFN or poly-IC induces phosphorylation and cytoplasmic-to-nuclear translocation of IRF3, which seems essential for its function in that phosphomimic active IRF3 exhibits stronger transactivation than wild type IRF3. Finally, overexpression of fish IRF3 activates production of IFN that in turn triggers ISG transcription through Stat1 pathway, whereas transfection of dominant negative mutant IRF3-DN abrogates poly-IC induction of ISGs, probably owing to blockade of IFN production. Therefore, regulation of IFN response by vertebrate IRF3 is another ancient trait. These data provide evidence of the evolving function of vertebrate IRF3 on regulating IFN response.

Molecular cloning of vitellogenin gene and mRNA expression by 17alpha-ethinylestradiol from slender bitterling

Indigenous aquatic population such as fish could be used as a successful test species for evaluating the ecological effects in aquatic environment. In the present study, vitellogenin (Vtg) from slender bitterling (Acheilognathus yamatsutae), an indigenous aquatic species in Korea, was cloned and sequenced to determine if the Vtg gene possesses an important characteristic so as to act as a sensitive biomarker for estrogenic endocrine disrupting chemicals (EEDCs). The sbVtg cDNA is 5010 bp in length, containing a 4653 bp open reading frame, which encodes 1550 amino acid residues. The sbVtg cDNA was divided into lipovitellin heavy chain (LvH), phosvitin (Pv), lipovitellin light chain (LvL) as well as a beta'-component (beta'-c) domain, and belongs to VtgAo2. SbVtg has conserved important sequences for Vtg functions such as signal peptide, VtgR-binding region, and disulfide bond formation, all of which are consistent with those of other teleosts. In addition, the male slender bitterling aqueous exposed to 17 alpha-ethinylestradiol (EE2, 12.5, 25, and 50 ng/L) produced a statistically significant and concentration-dependent increase in hepatic Vtg mRNA expression, which showed a similar pattern to biliary estrogenic activity, measured by ERE-reporter gene assay. Thus, this study clearly indicates that the induction of Vtg in slender bitterling might be a suitable biomarker in toxicological research of EEDCs.

The fight between the teleost fish immune response and aquatic viruses

Teleost fish represent a transition point on the phylogenetic spectrum between invertebrates that depend only on innate immunity and mammals that heavily depend on adaptive immunity. The major mechanisms of the teleost fish innate immune response are suggested to be similar to mammals, although fine details of the process require further studies. Within the innate immune response the type I interferon (IFN) system is an essential innate antiviral component that protects fish from some virus infections. The current progress of cloning and functional characterization of fish antiviral genes is promising in further elucidation of the fish antiviral response. The adaptive immune system of fish utilizes cellular components more or less similar to mammals. Teleost fish produce IgM as a primary antibody response and lack isotype switching to mount virus-specific antibodies during the infection process. Despite this, the development of successful fish rhabdoviral vaccines suggest that vaccination may prove to be an effective way of promoting fish adaptive immune responses to viruses. This paper reviews the bony fish antiviral response with specific discussion on the evolutionary mechanisms that allow aquatic viruses to co-exist with their host. Detailed aspects of the teleost type I IFN system are also addressed.

Fish virus-induced interferon exerts antiviral function through Stat1 pathway

Virus-induced interferons (IFNs) have been identified in various fish species and display antiviral activities similar to mammalian type I IFNs. However, apart from the mammalian IFN system, the IFN signaling pathway remains largely unknown. Using transient transfection and recombinant protein, we are reporting in this study that a crucian carp (Carassius auratus L.) IFN exhibits strong antiviral activity against grass carp hemorrhagic virus (GCHV) infection and also mediates Poly I:C-induced antiviral response, which correlates with its ability to induce a set of IFN-stimulated genes (ISGs). Strikingly, overexpression of wild-type Stat1 increases the effects of IFN on both the expression of ISGs and the inhibition of virus infection, whereas a dominant negative mutant of Stat1 (Stat1-Delta C), which lacks of the C-terminal transcriptional activation domain (TAD), inhibits the antiviral activity of IFN and reduces the expression of ISGs, demonstrating that fish IFN induces the expression of ISGs and host antiviral response through Stat1 pathway reminiscent that of mammalian IFNs. Significantly, unlike mammalian type I IFNs, recombinant fish IFN is able to upregulate IFN itself, which is enhanced by overexpression of Stat1 but impaired by knockdown of Stat1, indicating a positive feedback loop in regulation of IFN itself. These results provide strong evidence for the existence of an evolutionary conserved Stat1 pathway between fish and mammals, which is indispensable for fish virus-induced IFN antiviral response.

Global characterization of interferon regulatory factor (IRF) genes in vertebrates: glimpse of the diversification in evolution

BACKGROUND

Interferon regulatory factors (IRFs), which can be identified based on a unique helix-turn-helix DNA-binding domain (DBD) are a large family of transcription factors involved in host immune response, haemotopoietic differentiation and immunomodulation. Despite the identification of ten IRF family members in mammals, and some recent effort to identify these members in fish, relatively little is known in the composition of these members in other classes of vertebrates, and the evolution and probably the origin of the IRF family have not been investigated in vertebrates.

RESULTS

Genome data mining has been performed to identify any possible IRF family members in human, mouse, dog, chicken, anole lizard, frog, and some teleost fish, mainly zebrafish and stickleback, and also in non-vertebrate deuterostomes including the hemichordate, cephalochordate, urochordate and echinoderm. In vertebrates, all ten IRF family members, i.e. IRF-1 to IRF-10 were identified, with two genes of IRF-4 and IRF-6 identified in fish and frog, respectively, except that in zebrafish exist three IRF-4 genes. Surprisingly, an additional member in the IRF family, IRF-11 was found in teleost fish. A range of two to ten IRF-like genes were detected in the non-vertebrate deuterostomes, and they had little similarity to those IRF family members in vertebrates as revealed in genomic structure and in phylogenetic analysis. However, the ten IRF family members, IRF-1 to IRF-10 showed certain degrees of conservation in terms of genomic structure and gene synteny. In particular, IRF-1, IRF-2, IRF-6, IRF-8 are quite conserved in their genomic structure in all vertebrates, and to a less degree, some IRF family members, such as IRF-5 and IRF-9 are comparable in the structure. Synteny analysis revealed that the gene loci for the ten IRF family members in vertebrates were also quite conservative, but in zebrafish conserved genes were distributed in a much longer distance in chromosomes. Furthermore, all ten different members are clustered in respectively different clades; but the IRF-11 was clustered with one in sea urchin.

CONCLUSIONS

In vertebrates, the ten well-characterized IRF family members shared a relatively high degree of similarity in genomic structure and syntenic gene arrangement, implying that they might have been evolved in a similar pattern and with similar selective pressure in different classes of vertebrates. Genome and/or gene duplication, and probably gene shuffling or gene loss might have occurred during the evolution of these IRF family members, but arrangement of chromosome or its segment might have taken place in zebrafish. However, the ten IRF family members in vertebrates and those IRF-like genes in non-vertebrate deuterostomes were quite different in those analyzed characters, as they might have undergone different patterns of evolution.

Interferon regulatory factor-2 in orange-spotted grouper (Epinephelus coioides): gene, inductive expression pattern and subcellular localization

Interferon regulatory factor 2 (IRF-2) is a multifunctional transcription factor which exhibits both transcriptional activating and repressing activities in the IRF family. In this study, we report an IRF-2 gene isolated from orange-spotted grouper (Epinephelus coioides). The 1854bp full-length cDNA sequence of EcIRF-2 has been cloned, encoding a putative peptide of 336 amino acids which is highly consistent with the feature of IRF family members. The genomic fragment of EcIRF-2 contains nine exons and eight introns, spanning over approximate 8.8kb. The expression of EcIRF-2 gene was detected in various tissues of healthy orange-spotted grouper and in four tissues after being challenged with poly I:C or LPS. EcIRF-2 gene is ubiquitously expressed in various healthy fish tissues and is up-regulated in vivo in response to poly I:C or LPS. Subcellular localization analysis of EcIRF-2 suggests it is an intranuclear protein in the fish cells. We believe this research is the first report of fish IRF-2 protein localization. The results in this research establish the base for further study of function mechanism of IRF family members in orange-spotted grouper.

Identification of estrogen-like effects and biologically active compounds in river water using bioassays and chemical analysis

The Nackdong River is the longest river in South Korea and passes through major cities that have several industrial complexes, including chemical, electric, and petrochemical complexes, and municipal characteristics such as apartment complexes. Along the river, the Gumi region has an electric industrial complex and an apartment complex that may be possible point sources of xenoestrogens such as phenolic compounds. To identify the causative chemicals for estrogenic activity in the river water of this region, bioassay-directed chemical analysis was performed. All samples from six sampling sites (an upstream point: S1; hot spot points: S2-1, S2-2, and S2-3; and downstream points: S3, and S4) showed estrogenic activity in the E-screen assay, with bio-EEQs (17beta-E(2)-equivalent quantities) ranging from 25.35-677.15 pg/L. Samples from S2-2, the sampling point downstream of the junction of stream water, and domestic and industrial wastewater, contained the highest estrogenic activity. Since the bio-EEQ of the organic acid fraction (F2) of the S2-2 sample had the highest activity (823.25 pg-EEQ/L) and F2 may contain phenolic compounds, GC-MS analyses for phenolic xenoestrogens were conducted with the organic acid fractions of the river water samples. Six estrogenic phenolic chemicals, 4-NP, BPA, 4-t-OP, 4-t-BP, 4-n-OP, and 4-n-HTP, were detected, with the highest concentrations (I-EEQ) found in S2-2 (231.80 pg/L). Among these phenolic chemicals, 4-NP was the most potent estrogen (bio-EEF; 8.12 x1 0(-5)) and acted as a full agonist. Furthermore, 4-NP was present at levels (2.0 microg/L in S2-2) that can induce VTG induction in fish (>1 microg/L). In addition, we confirmed that river water (S2-2) significantly increased serum VTG levels in crucian carp (Carassius auratus) in a fish exposure experiment under laboratory conditions. Therefore, phenolic xenoestrogens, especially 4-NP, may be the main causative compounds responsible for the estrogenic effect on the Nackdong River.

Molecular cloning of CYP1A gene and its expression by benzo(a)pyrene from goldfish (Carassius auratus)

We cloned and sequenced the cytochrome P450 1A (CYP1A) gene from goldfish (Carassius auratus). It has a 1581 bp open reading frame that encodes a 526 amino acid protein with a theoretical molecular weight of 59.02 kDa. The CYP1A amino acid sequence clusters in a monophyletic group with other fish CYP1As, and more closely related to zebrafish CYP1A (91% identity) than to other fish CYP1As. Exposure to benzo(a)pyrene (BaP) by intraperitoneal injection increased biliary BaP metabolites and liver CYP1A gene expression. BaP exposure also increased CYP1A gene expression in extrahepatic organs, including intestine, and gill, which are sensitive to aqueous and dietary exposure to Arylhydrocarbon receptor (AhR) agonists. Therefore, goldfish CYP1A identified in this study offers basic information for further research related to biomarker use of CYP1A of goldfish.

Identification and characterization of interferon regulatory factor-1 from orange-spotted grouper (Epinephelus coioides)

Interferon-regulatory factor 1 (IRF-1) is the first member of IRF family, which is involved in many biological processes such as immune response, antiviral defense, cell growth regulation, and apoptosis. In this study, an IRF-1 gene, EcIRF-1, was isolated and characterized from orange-spotted grouper (Epinephelus coioides). The full-length cDNA of EcIRF-1 is 1,730 bp, including an open reading frame of 906 bp, a 5'-terminal untranslated region (5'-UTR) of 153 bp, and a 3'-UTR of 671 bp. The EcIRF-1 gene consists of 10 exons and 9 introns, spanning over approximate 4.3 kb of genomic sequence. The 5'-UTR sequence contains an exon and an intron, and the 3'-UTR sequence is included in the last exon. Expression analysis by real-time PCR reveals that the EcIRF-1 gene is ubiquitously expressed in various healthy fish tissues, whereas its expression is upregulated in vivo in response to polyinosinic-polycytidylic acid or lipopolysaccharide stimulation. Subcellular localization analysis shows the EcIRF-1 is an intranuclearly localized and immobile protein in the cultured fish cells. Data presented in this paper provide an important base to further understand EcIRF-1 gene function and its regulation associated with interferon immune system in orange-spotted grouper.

Structural and functional studies of an IRF-7-like gene from Atlantic salmon

Interferon regulatory factor 7 (IRF-7) plays a crucial role in virus-induced activation of interferon-alpha/beta transcription in mammals. This work describes a structural and functional homologue of mammalian IRF-7 from Atlantic salmon. The cloned gene encodes a putative protein of 415 amino acids (aa), which groups with mammalian IRF-7 and other fish IRF-7-like proteins in a phylogenetic analysis of vertebrate IRFs. Using an IFN promoter-luciferase assay we showed that salmon IRF-7 gave increased promoter activity after poly I:C stimulation. Transcript levels of IRF-7 were measured by real-time RT-PCR and compared to those of signal transducer and activator of transcription 1 (STAT1), which is important for transcriptional activation of IFN stimulated genes. Recombinant salmon IFN-alpha1 and poly I:C proved to be potent inducers of IRF-7 in Atlantic salmon TO cells, and poly I:C also induced the gene in head kidney and liver of Atlantic salmon. STAT1 was also induced by IFN, but was only weakly induced by poly I:C stimulation in vitro. Differences in transcription kinetics between IRF-7 and STAT1 thus indicate that the genes are regulated through different pathways. Finally, infection of TO cells with infectious salmon anemia virus (ISAV) induced early synthesis of STAT1 mRNA, whereas IRF-7 transcripts were upregulated much later. This indicates that ISAV has mechanisms to antagonize IRF-7 transcription and thus also the IFN system in Atlantic salmon.