Identification of type I IFNs and their receptors in a cyprinid fish, the topmouth culter Culter alburnus

Geographical region traceability of wild topmouth culter (Culter alburnus) from Xingkai Lake based on muscle quality and aroma profiles

The wild topmouth culter (Culter alburnus) from Xingkai Lake (XKL) is highly regarded for its delicious taste and unique flavor. In this study, based on muscle quality and aroma analysis, we first differentiated the XKL population from three wild populations in Heilongjiang Province and one artificially cultured population (from Xingkai Lake). Compared with the other populations, the XKL population has a significantly higher crude protein content, essential amino acid content, delicious amino acid content, and n-3/n-6 PUFA ratio. Additionally, it exhibits superior hardness, elasticity, chewiness, recoverability, and viscosity. E-nose detection analysis revealed that W1S, W2S, and W3S were the potential sensors contributing the most to the differences among the five populations. HS-SPME-GC-MS and multivariate regression analysis showed that 21 volatile flavor compounds were identified as key markers for geographical identification of the Xingkai Lake region. These findings will provide guidance for the geographical traceability and identification of the XKL population.

Transcriptome-wide analyses of early immune responses in lumpfish leukocytes upon stimulation with poly(I:C)

Background

Both bacterial and viral diseases are a major threat to farmed fish. As the antiviral immune mechanisms in lumpfish (Cyclopterus lumpus L.) are poorly understood, lumpfish leukocytes were stimulated with poly(I:C), a synthetic analog of double stranded RNA, which mimic viral infections, and RNA sequencing was performed.

Methods

To address this gap, we stimulated lumpfish leukocytes with poly(I:C) for 6 and 24 hours and did RNA sequencing with three parallels per timepoint. Genome guided mapping was performed to define differentially expressed genes (DEGs).

Results

Immune genes were identified, and transcriptome-wide analyses of early immune responses showed that 376 and 2372 transcripts were significantly differentially expressed 6 and 24 hours post exposure (hpe) to poly(I:C), respectively. The most enriched GO terms when time had been accounted for, were immune system processes (GO:0002376) and immune response (GO:0006955). Analysis of DEGs showed that among the most highly upregulated genes were TLRs and genes belonging to the RIG-I signaling pathway, including LGP2, STING and MX, as well as IRF3 and IL12A. RIG-I was not identified, but in silico analyses showed that genes encoding proteins involved in pathogen recognition, cell signaling, and cytokines of the TLR and RIG-I signaling pathway are mostly conserved in lumpfish when compared to mammals and other teleost species.

Conclusions

Our analyses unravel the innate immune pathways playing a major role in antiviral defense in lumpfish. The information gathered can be used in comparative studies and lay the groundwork for future functional analyses of immune and pathogenicity mechanisms. Such knowledge is also necessary for the development of immunoprophylactic measures for lumpfish, which is extensively cultivated for use as cleaner fish in the aquaculture for removal of sea lice from Atlantic salmon (Salmo salar L.).

Molecular characterization of nineteen cytokine receptor family B (CRFB) members, CRFB1, CRFB2, CRFB4-17, with three CRFB9 and two CRFB14 in a cyprinid fish, the blunt snout bream Megalobrama amblycephala

The class II cytokine receptor family members are receptors of class 2 helical cytokines in mammals, and are named cytokine receptor family B (CRFB) in fish. In zebrafish, sixteen members, including CRFB1, CRFB2 and CRFB4-17 were reported. With the availability of genome sequence, a total of nineteen CRFBs was identified in the blunt snout bream (Megalobrama amblycephala), including CRFB1, CRFB2, CRFB4-17 with the presence of three CRFB9 isoforms, and two CRFB14 isoforms. These CRFB molecules contain well conserved features, such as fibronectin type III (FNIII) domain, transmembrane and intracellular domains as other class II cytokine receptors, and are phylogenetically grouped into thirteen clades with their homologues from other species of fish. The CRFB genes were constitutively expressed in organs/tissues examined in the fish. The finding of more CRFB members in the bream may provide clues to understand possible receptor-ligand interaction and their diversity from an evolutionary point of view.

Structural and Functional Analyses of Type I IFNa Shed Light Into Its Interaction With Multiple Receptors in Fish

Teleost type I interferons (IFNs) are categorized into group I and II subgroups that bind to distinct receptors to activate antiviral responses. However, the interaction between ifn ligands and receptors has not fully been understood. In this study, the crystal structure of grass carp [Ctenopharyngodon idella (Ci)] IFNa has been solved at 1.58Å and consists of six helices. The CiIFNa displays a typical structure of type I IFNs with a straight helix F and lacks a helix element in the AB loop. Superposition modeling identified several key residues involved in the interaction with receptors. It was found that CiIFNa bound to cytokine receptor family B (CRFB) 1, CRFB2, and CRFB5, and the three receptors could form heterodimeric receptor complexes. Furthermore, mutation of Leu27, Glu103, Lys117, and His165 markedly decreased the phosphorylation of signal transducer and activator of transcription (STAT) 1a induced by CiIFNa in the Epithelioma papulosum cyprini (EPC) cells, and Glu103 was shown to be required for the CiIFNa-activated antiviral activity. Interestingly, wild-type and mutant CiIFNa proteins did not alter the phosphorylation levels of STAT1b. Our results demonstrate that fish type I IFNs, although structurally conserved, interact with the receptors in a manner that may differ from mammalian homologs.

Four type I IFNs, IFNa1, IFNa2, IFNb, IFNc, and their receptor usage in an osteoglossomorph fish, the Asian arowana, Scleropages formosus

In fish, type I IFNs are classified into three groups, i.e. Group I, Group II and Group III, which are further divided into seven subgroups according to the number of conservative cysteines, phylogenetic relationship, and probably their receptor complexes. In the present study, four type I IFNs and four cytokine receptor family B members (CRFBs) were identified in the Asian arowana, Scleropages formosus, an ancient species in the Osteoglossomorpha with commercial and conservation values. According to multiple sequence alignment and phylogenetic relationship, the four type I IFNs are named as IFNa1, IFNa2, IFNb and IFNc, with the former two belonging to Group I, and the latter two to Group II. The four receptors are named as CRFB1, CRFB2, CRFB5a and CRFB5b. The IFNs and their possible receptor genes are widely expressed in examined organs/tissues, and are induced following the stimulation of polyinosinic polycytidylic acid (polyI:C) in vivo. It was found that IFNa1, IFNa2, IFNb and IFNc use preferentially the receptor complexes, CRFB1 and CRFB5b, CRFB1 and CRFB5b, CRFB2 and CRFB5a, and CRFB2 and CRFB5b, respectively, indicating the evolutionary diversification in the interaction of type I IFNs and their receptors in this ancient fish species, S. formosus.

Comprehensive comparison of thirteen kinds of cytokine receptors from the endangered fish Chinese sturgeon (Acipenser sinensis)

The interferon receptor system in teleost fish is more complex than that in mammals. In the present study, we identified 13 cytokine receptor genes (10 interferon receptor genes and 3 IL10R2-like genes) from Chinese sturgeon (Acipenser sinensis) using RNA-sequencing. Sequence analysis indicated that these receptors had conserved domains, including signal peptides, FNⅢ, and transmembrane domains. Phylogenetic analysis suggested that they belonged to the cytokine receptor family. In the present study, we named them IFNAR1-like (CRFB5a, CRFB5b), IFNAR2-like (CRFB3a, CRFB3b), IFNGR1-like (IFNGR1), IFNGR2-like (CRFB6a, CRFB6b/IFNGR2-1, CRFB6c/IFNGR2-2, CRFB6d/IFNGR2-3, CRFB6e/IFNGR2-4) and IL10R2-like (CRFB4a, CRFB4b, CRFB4c), respectively. Constitutive expression analysis revealed that these receptor genes had potential functions in immune and non-immune tissue compartments. After stimulating with Poly (I:C), the expression fold changes of CRFB3a, CRFB4a, CRFB4b, CRFB5b, and CRFB6e/IFNGR2-4 in Chinese sturgeon were higher than those of other receptor genes, which revealed that these five genes had important functions in the immune process to resist virus invasion in the host. After stimulating with IFN gamma, the expression fold changes of CRFB3a, CRFB4a, and CRFB6b/IFNGR2-1 were higher than those other receptor genes. Based on other teleost fish interferon receptor models, we speculated that IFNAR1-like (CRFB5a, CRFB5b) and IFNAR2-like (CRFB3a, CRFB3b), comprised Chinese sturgeon type Ⅰ IFN receptors; and IFNGR1-like (IFNGR1) and IFNGR2-like (CRFB6/IFNGR2) comprised Chinese sturgeon type Ⅱ IFN receptors.

Type I interferons in ray-finned fish (Actinopterygii)

Interferons (IFNs) are proteins of vital importance in the body's immune response. They are formed in different types of cells and have been found in fish, amphibians, reptiles and mammals. Two types of IFN have been found in ray-finned fish (Superclass: Osteichthyes, Class: Actinopterygii) so far, i.e. IFN type I (IFN I) and IFN type II (IFN II), while the presence of IFN type III (IFN III), which is found in phylogenetically older cartilaginous fishes, was not confirmed in this taxonomic group of vertebrates. Currently, type I IFN in Actinopterygii is divided into three groups, I, II and III, within which there are subgroups. These cytokines in these animals show primarily antiviral activity through the use of a signalling pathway JAK-STAT (Janus kinases - Signal transducer and activator of transcription) and the ability to induce ISG (IFN-stimulated genes) expression, which contain ISRE complexes (IFN-stimulated response elements). On the other hand, in Perciformes and Cyprinidae, it was found that type I/I interferons also participate in the antimicrobial response, inter alia, by inducing the expression of the inducible nitric oxide synthase (iNOS) and influencing the production of reactive oxygen species (ROS) in cells carrying out the phagocytosis process.