Characterization and expression of the CXCR1 and CXCR4 in miiuy croaker and evolutionary analysis shows the strong positive selection pressures imposed in mammal CXCR1

METTL16, an evolutionarily conserved m6A methyltransferase member, inhibits the antiviral immune response of miiuy croaker (Miichthys miiuy)

Methyltransferase like-16 (METTL16) is an m6A RNA methylation transferase that is known to methylate U6 snRNA and pre-mRNA of S-adenosylmethionine synthase but has been poorly studied in fish. In this study, METTL16 was identified in miiuy croaker (Miichthys miiuy). We first performed bioinformatics analysis of the miiuy croaker METTL16 (mmiMETTL16). MmiMETTL16 and other vertebrates METTL16 have a relatively conserved MTD structural domain and gene structure, suggesting that their methylase activity may also be conservative. In healthy miiuy croaker, mmiMETTL16 was commonly expressed in the tested tissues. Expression of mmiMETTL16 in kidney, liver, and spleen tissues was significantly increased after poly(I:C) stimulation. Consistently, mmiMETTL16 was sensitive to poly(I:C) stimulation in miiuy croaker kidney cell (MKC), suggesting that METTL16 might participate in antiviral immunity. For further functional experiments, immunofluorescence of mmiMETTL16 presents in the nucleus in kidney cells. In addition, the overexpression of mmiMETTL16 could significantly increase the overall m6A level of MKC cells, which shows that the function of METTL16 as methyltransferase is conservative in miiuy croaker. Last, mmiMETTL16 can inhibit the expression of TNF-α, IFN-1, Mx1, and ISG15, suggesting that mmiMETTL16 can suppress the immune response caused by viral stimulation. In summary, studies on mmiMETTL16 will contribute to future studies on the role of METTL16 and potential mechanisms of the m6A regulation network in the teleost immune system.

Molecular cloning, characterization and expression analysis of CXCR3a and CXCR3b from Nile tilapia (Oreochromis niloticus)

The CXC chemokine receptors (CXCRs) are members of the seven transmembrane (7-TM) G-protein-coupled receptor superfamily that involves innate and adaptive immune systems. In this study, CXCR3a and CXCR3b from Nile tilapia (Oreochromis niloticus) were cloned and identified, designated as OnCXCR3a and OnCXCR3b. The open reading frames of OnCXCR3a and OnCXCR3b were 1074 and 1080 bp, encoding the predicted proteins of 357 and 359 amino acids, respectively. Multiple alignment analysis of OnCXCR3a- and OnCXCR3b-deduced protein sequences with the mammalian and bird sequences indicated the presence of typical structural features of chemokine receptors, including a 7-TM domain and conserved motifs. Quantitative real-time PCR analysis revealed that OnCXCR3a and OnCXCR3b were constitutively expressed in a wide range of tissues. When stimulated with Streptococcus agalactiae, Aeromonas hydrophila, polyinosinic:polycytidylic acid and lipopolysaccharide in vivo or in vitro on leukocytes, the mRNA levels of OnCXCR3a and OnCXCR3b were significantly upregulated. Overall, these results indicated that OnCXCR3s might be involved in host immune responses in Nile tilapia.

Circular RNA circRara promote the innate immune responses in miiuy croaker, Miichthys miiuy

With the in-depth study of circRNA, more and more biological studies have shown that circRNAs play an important role in mammals, such as cell proliferation, apoptosis, invasion, development and disease state. However, the regulatory mechanism of circRNA in lower vertebrates remains unclear. Here, we found a new circular RNA and named it circRara. We carried out the experimental study on its antiviral and antibacterial response, cell proliferation and activity. The results showed that circRara had a positive regulatory effect on the antiviral and antibacterial response, cell proliferation and activity in miiuy croaker. First, we found that the expression of circRara could be up-regulated under the stimulation of LPS and poly (I: C), but not the expression of linear Rara. In addition, the increase of circRara can increase the production of inflammatory factors and antiviral genes, which was confirmed by double luciferase reporter gene experiment and qPCR. These results will help to further understand the immunomodulatory mechanism of circRNA in teleost fish.

The long noncoding RNA LTCONS5539 up-regulates the TRAF6-mediated immune responses in miiuy croaker (Miichthys miiuy)

With the further study of long noncoding RNAs (lncRNAs), an increasing number of biological studies have demonstrated that lncRNAs are involved in various physiological processes, including cell proliferation, apoptosis, invasion, development and disease states. However, unlike mammals, little is known about the role of lncRNAs in the innate immunity of teleost fish. Here, we identify a lncRNA, named LTCONS5539, as critical role in the antiviral and antibacterial response of miiuy croaker and the results showed that lncRNA LTCONS5539 plays a critical regulatory role on TRAF6. Firstly, we found that LPS and poly(I:C) can up-regulate the expression of lncRNA LTCONS5539. Elevated lncRNA LTCONS5539 is capable of increasing the production of inflammatory factors and antiviral genes. Furthermore, the over-expression of lncRNA LTCONS5539 increases the expression of TRAF6 which was confirmed by qPCR and western blotting. On these foundations, we also proved that lncRNA LTCONS5539 modulates innate immunity through TRAF6-mediated immune responses through dual luciferase reporter assay. These results will help to further understand the immunomodulatory mechanisms of lncRNA in teleost fish.

Long Noncoding RNA MIR122HG Inhibits MAVS-Mediated Antiviral Immune Response by Deriving miR-122 in Miiuy Croaker (Miichthys miiuy)

Long noncoding RNAs (lncRNAs) function as micro regulators to impact gene expression after multiple pathogen infections, which have been largely studied in the last few years. Although lncRNA studies on lower vertebrates have received less attention than those on mammals, current studies suggest that lncRNA plays an important role in the immune response of fish to pathogen infections. Here, we studied the effect of MIR122HG as the host gene of miR-122 and indirectly negatively regulate MAVS-mediated antiviral immune responses in miiuy croaker (Miichthysmiiuy). We found that poly(I:C) significantly increases the host MIR122HG expression. The increased MIR122HG expression inhibited the production of the antiviral immune-related genes IFN-1, ISG15 and Viperin upon SCRV treatment. In addition, MIR122HG can act as a pivotally negative regulator involved in the MAVS-mediated NF-κB and IRF3 signaling pathways, which can effectively avoid an excessive immune response. Additionally, we found that MIR122HG can promote the replication of SCRV. Our study provides evidence about the involvement of lncRNAs in the antiviral immune response of fish and broadens the understanding of the function of lncRNAs as a precursor miRNA in teleost fish.

MicroRNA-103 and microRNA-190 negatively regulate NF-κB-mediated immune responses by targeting IL-1R1 in Miichthys miiuy

Accumulating evidence has demonstrated that microRNAs (miRNAs) regulate various physiological and pathological processes at the transcriptional level, thus called novel regulators in immune response. In this study, we used bioinformatics and functional experiments to determine the role of miR-103 and miR-190 in the regulation of IL-1R1 gene involved in the immune and inflammatory responses in miiuy croakers. First, we predicted the target genes of miR-103 and miR-190 through bioinformatics and found that IL-1R1 is a direct target gene of miR-103 and miR-190. This was further confirmed by the dual-luciferase reporter assay that the over-expression of miR-103, miR-190 mimics and the pre-miR-103, pre-miR-190 plasmids inhibit the luciferase levels of the wild-type of IL-1R1 3'UTR. miR-103 and miR-190 inhibitors increase the luciferase levels of IL-1R1-3'UTR. Additionally, we found that miR-103 and miR-190 could negatively regulate the mRNA expression of IL-1R1. Importantly, we demonstrated that miR-103 and miR-190 significantly inhibit the NF-κB signaling pathway by targeting IL-1R1 upon LPS stimulation. Collectively, these results provide strong evidence for an important regulatory mechanism of miR-103 and miR-190 targeting the IL-1R1 gene, thereby preventing excessive inflammatory immune responses from causing autoimmunity.

Genomic organization, evolution and functional characterization of caspase-2 and caspase-8 in miiuy croaker (Miichthys miiuy)

As the central link and executor of cell apoptosis, the caspase protease family has received extensive attention in recent years. However, the genetic characteristics and immune functions of some caspases are still unknown in fish. In our study, we cloned the full-length caspase-2 (mmCasp2) and caspase-8 (mmCasp2) of miiuy croaker, then we analyzed characteristics and functions of these two genes which are upstream of the apoptosis cascade reaction. Mmcasp2 and mmCasp8 exhibited a conserved domain (CASc), and the different part is that the mmCasp2 has a CARD domain, while mmCasp8 have two DED domains. Sequence and evolution analysis results showed that caspase-2 is more conservative than caspae-8 in the process of evolution. Cellular localization analysis showed that the distribution of mmCasp2 and mmCasp2 was in cytoplasm. The real-time PCR analysis showed that these two caspases are constitutively expressed in different tissues, and the expression of mmCasp2 and mmCasp8 were up-regulated in the liver, spleen, and kidney after infection with V. anguillarum. Lastly, qRT-PCR and Luciferase assays analysis showed that mmCasp2 and mmCasp8 can inhibit the NF-кB pathway. In general, we systematically analyzed the structure, evolution and related functional experiments of the caspase-2 and caspase-8 in miiuy croaker, which will help further understand the role caspase family plays in the apoptosis and immune response.

Characterization of MDA5 and microRNA-203 negatively regulates the RLR signaling pathway via targeting MDA5 in miiuy croaker

MDA5 is a member of retinoic acid-inducible gene I (RIG-I)-like receptors (RLR receptors), which may play a crucial role in the immune regulation process. Recently, microRNAs (miRNAs) have been shown to act as an important regulator in the RLRs signaling pathway. Additionally, the MDA5 gene, as a significant cytosolic pathogen recognition receptor (PRR), its characteristics and functions have been extensively investigated, while less research has been done on the mechanisms of MDA5-miRNA mediated gene regulation. In this study, the evolution and functional characterization of MDA5 from miiuy croaker (mmiMDA5) were characterized. Comparative genomic analysis demonstrated that the ascidiacea and superclass do not have the MDA5 gene in the process of evolution. MDA5 contains four structural domains: CARD, ResIII, Helicase C, and RIG-I C-RD. The MDA5 was ubiquitously expressed in all tested miiuy croaker tissues. Moreover, the expressions were significantly up-regulated after stimulation with poly (I: C), which indicated that MDA5 might be involved in the antiviral immune response. The bioinformatics predicted programs have indicated that miR-203 has a direct negative regulatory effect on MDA5 in miiuy croaker. Furthermore, the dual-luciferase reporter assay have showed that miR-203 was the direct negative regulator of MDA5 in miiuy croaker. This study is the first to demonstrate that miRNA can suppress cytokines by regulating the RLR signaling pathway in teleost fish, providing some new ideas for studying miRNA-mediated regulation of immune responses in mammals.

Genome-wide identification and analysis of chemokine receptor superfamily in miiuy croaker, Miichthys miiuy

The chemokine receptor (ChemR) superfamily, which is divided into 4 subfamilies (CXCR, CCR, XCR, and CX3CR), is the main receptors of chemokines in innate immune responses. In the current study, we have identified 27 ChemRs in miiuy croaker: 13 CCR genes, 11 CXCR genes, and 3 XCR genes. Multiple characteristics of these genes, including phylogeny, gene structures, conserved motifs, chromosome locations, evolutionary mechanism, and expression levels upon the bacterial challenge were analyzed. Gene structure and location analysis showed that all ChemR genes contain fewer introns (≤4) and they are unevenly distributed on the 12 chromosomes. And the XCR subfamily of miiuy croaker don't have the DRY motif of ChemR. Phylogenetic and synteny analysis showed that these genes experienced tandem and segmental duplication event in several species, and tandem duplication might be the main expansion way in miiuy croaker. The major ChemRs of each orthologous group in vertebrates were selected for molecular evolution analysis, the results of which indicated that compared with vertebrates, ChemRs of teleost fishes may have a relatively high evolutionary dynamic. In addition, a total of 21 positively selected codons were detected in vertebrate ChemRs under Model 8. RNA-Seq analysis and qRT-PCR verification demonstrated that CXCR3.2, CXCR5, and XCR1 genes were up-regulated significantly upon the Vibrio harveyi infection. These results provide valuable information for investigating the evolutionary relationships of chemokine receptor superfamily in miiuy croaker and laid the basis for further functional analysis.

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

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

Diurnal expression of CXC receptors 4 (CXCR4) and CXC chemokine ligand 12 (CXCL12) in Pelteobagrus vachellii

The CXC chemokine ligand 12/CXC receptor 4 ligand/receptor interaction is the most ancient chemokine system in vertebrates, and it plays a pivotal role in the immune system's response against bacterial infection. In the current study, 1211 bp CXCR4 and 937 bp CXCL12 genes, which encode 364 and 99 amino acids, respectively, were isolated. Within the 24-hour light/dark cycle, the maximum of CXCR4 in the intestine, spleen, and anterior kidney of Pelteobagrus vachellii occurs at 8:00, 16:00, and 16:00, respectively. The maximum of CXCL12 in the intestine, spleen, and anterior kidney of P. vachellii occurs at 20:00, 12:00, and 20:00, respectively. CXCR4 and CXCL12 expressions showed 24-hour variation, which contributed to understanding of the immune rhythm of the teleost.

Nile tilapia CXCR4, the receptor of chemokine CXCL12, is involved in host defense against bacterial infection and chemotactic activity

CXC chemokine receptor 4 (CXCR4), a member of seven-transmembrane (7-TM) G-protein-coupled receptor superfamily, is the receptor of the CXC chemokine ligand 12 (CXCL12), and plays important roles in host defense and inflammation. In the current study, we cloned and identified a homolog of CXCR4 from Nile tilapia (Oreochromis niloticus), designated as OnCXCR4. The open reading frame of OnCXCR4 is 1149 bp encoding a peptide of 382 amino acids, and the predicted molecular weight is 42.65 kDa OnCXCR4 shares common features of CXCR4 family, including a 7-TM domain and a characteristic CXC motif (containing CYC). Expression analysis showed that OnCXCR4 constitutively expresses in various tested tissues of Nile tilapia, with the highest level in the anterior kidney. When stimulated with Streptococcus agalactiae, Aeromonas hydrophila, Poly(I:C), or LPS in vivo and in vitro, the expression of OnCXCR4 was significantly regulated. AMD3100, a CXCR4 antagonist, could not only inhibit the chemotactic activity of the recombinant OnCXCL12 protein on the leukocytes from anterior kidney, but also reduce the expression of OnCXCR4 significantly. Taken together, these results of our study above indicate that OnCXCR4 may play important roles in host defense against bacterial infectionin in Nile tilapia, and being a receptor of OnCXCL12 to exert functions.

Molecular cloning, characterization and expression analysis of MHCI and chemokines CXCR3 and CXCR4 gene from freshwater carp, Catla catla

The immune system with large number of molecules protects the host against a plethora of continuously evolving microbes. Major histocompatibility complex (MHC) molecules serve as cardinal elements of the adaptive immune system responsible for the activation of the adaptive immunity in the host. The present study reports MHCI molecule in freshwater carp, Catla catla, and its differential expression in immunologically relevant tissues post-infection with Gram-negative and Gram-positive bacteria. The MHCI sequence of C. catla had 502 bp nucleotides encoding putative 146 amino acids. The phylogenetic analysis exhibited its evolutionary conservation within the Cyprinidae family and formed a different clade with the higher vertebrates. Simultaneously, CXCR3 and CXCR4 chemokines were cloned and characterized for their expression in infected tissues. Analysis of immunologically relevant tissues of the infected fish exhibited an increase of MHCI gene expression and the down-regulation of CXCR3 and CXCR4 chemokines, indicating a tricky interaction between the innate and adaptive immune system. It was found that intestine, skin and spleen played a crucial role in the contribution of the defense activity which instigated the self-immunity. These immune activities can provide useful information to understand the interaction of self and non-self- immune system in freshwater fish, Catla catla.

Molecular characterization and expression analysis of Asian swamp eel (Monopterus albus) CXC chemokine receptor (CXCR) 1a, CXCR1b, CXCR2, CXCR3a, CXCR3b, and CXCR4 after bacteria and poly I:C challenge

The CXC chemokine receptors (CXCRs) play critical roles in innate and adaptive immune systems. In this study, six Asian swamp eel (Monopterus albus) CXCRs (MaCXCR1-4) were identified and their molecular characterization and expression patterns were analyzed. The open reading frames (ORFs) of MaCXCR1a, MaCXCR1b, MaCXCR2, MaCXCR3a, MaCXCR3b, and MaCXCR4 were 1074 bp (base pairs), 1080 bp, 1125 bp, 1146 bp, 1083 bp, and 1140 bp, and encoded proteins of 357 aa (amino acids), 359 aa, 374 aa, 381 aa, 360 aa, and 379 aa, respectively. All these CXCRs have seven conserved transmembrane domains and four cysteines (with the exception of MaCXCR3b). Multiple sequence alignment revealed that the MaCXCRs possess a typical G-protein receptor family 1 signature and a DRY motif. There are also one to four potential N-glycosylation sites in the extracellular regions of the MaCXCRs, mainly distributed in the N-terminus and extracellular hydrophilic loop (ECL) 2 region. Phylogenetic analysis demonstrated that the MaCXCRs were clustered together with homologous proteins from other fish. Taken together with the amino acid identity and similarity analysis, these results suggested that the MaCXCRs are conserved with other homologous genes, in which CXCR4 is more conserved than CXCR1-3. The MaCXCRs loci showed conserved synteny among teleost fish, and we found that human CXCR1 shares a common ancestor with fish CXCR1a. MaCXCRs were constitutively expressed in a wide range of tissues (especially in immune-related tissues) with different expression levels, suggesting that the MaCXCRs have different roles in un-stimulated tissues, and may play vital roles under normal conditions. MaCXCRs showed different fold changes in the spleen after Aeromonas veronii and polyinosinic-polycytidylic acid (poly I:C) challenge, which suggested that MaCXCR1a and MaCXCR3a have longer antiviral activities compared with their antibacterial functions, and that MaCXCR1b possesses stronger antiviral than antibacterial activity. MaCXCR4 may play vital roles during bacterial and viral infection; however, MaCXCR2 has relatively small effect in antibacterial and antiviral responses. The differential responses of these genes to bacteria and poly I:C implied the differences in the mechanisms of defense against viruses and bacteria.

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

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

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

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

A mini review on immune role of chemokines and its receptors in snakehead murrel Channa striatus

Chemokines are ubiquitous cytokine molecules involved in migration of cells during inflammation and normal physiological processes. Though the study on chemokines in mammalian species like humans have been extensively studied, characterization of chemokines in teleost fishes is still in the early stage. The present review provides an overview of chemokines and its receptors in a teleost fish, Channa striatus. C. striatus is an air breathing freshwater carnivore, which has enormous economic importance. This species is affected by an oomycete fungus, Aphanomyces invadans and a Gram negative bacteria Aeromonas hydrophila is known to cause secondary infection. These pathogens impose immune changes in the host organism, which in turn mounts several immune responses. Of these, the role of cytokines in the immune response is immense, due to their involvement in several activities of inflammation such as cell trafficking to the site of inflammation and antigen presentation. Given that importance, chemokines in fishes do have significant role in the immunological and other physiological functions of the organism, hence there is a need to understand the characteristics, activities and performace of these small molecules in details.

Characterization, expression, and evolutionary analysis of new TLR3 and TLR5M genes cloned from the spiny eel Mastacembelus armatus

Toll-like receptors (TLRs) play an important role in innate and adaptive immunity. Here, we identify two new TLRs from the spiny eel Mastacembelus armatus (TLR3 and membrane TLR5M). Both MaTLR3 and MaTLR5M were expressed in all tested tissues; expression was highest in liver and spleen, respectively. After infection with Vibrio parahaemolyticus, expression of both TLRs fluctuated and differed significantly from controls at several time points. The predicted three-dimensional model of the MaTLR3 and MaTLR5M proteins indicates that most sites under positive selection were located in the extracellular domains of TLRs. Evolutionary analysis detected positively selected sites in the ancestral lineages of vertebrates, amphibians and reptiles. Multiple ML methods recovered 10 positively selected sites in teleost TLR3 and 24 in TLR5M, and most sites were located in leucine-rich repeat domain, possibly related to an "arms-race" co-evolution with pathogens.

Molecular characterization and expression analysis of the large yellow croaker (Larimichthys crocea) chemokine receptors CXCR2, CXCR3, and CXCR4 after bacterial and poly I:C challenge

The large yellow croaker (Larimichthys crocea) has a well-developed innate immune system. We studied a component of this system, chemokine receptor CXCR family. In this study, we report the full-length open reading frames, as well as the identification and characterization of the chemokine receptor genes CXCR2 (LycCXCR2), CXCR3 (LycCXCR3), and CXCR4 (LycCXCR4) of large yellow croaker. We report that LycCXCR3 and LycCXCR4 are evolving neutrally according to PAML analyses. Quantitative real-time PCR analysis revealed that CXCR transcripts were expressed in all examined tissues. The expression of chemokine receptors LycCXCR2, LycCXCR3, and LycCXCR4 was elevated in the kidney, spleen, and particularly the liver of the large yellow croaker after challenge with Vibrio anguillarum and polyinosinic:polycytidylic acid (poly I:C). These results suggest that LycCXCR2, LycCXCR3, and LycCXCR4 may be important immune-related genes, playing crucial roles in immune defence against bacterial infection.

miRNA-8159 is involved in TLR signaling pathway regulation after pathogen infection by direct targeting TLR13 in miiuy croaker

Toll-like receptors (TLRs) play a crucial role in the recognition of immune reactions against invading pathogens. The molecular regulation mechanisms of TLR expression in aquatic organisms remain unclear. MicroRNAs (miRNAs) are small non-coding RNAs that are critical adjustors of immune signaling pathway at the post-transcriptional level and play critical roles in intricate networks of host-pathogen interactions and innate immunity. The critical role of TLRs in host defense for discerning certain kinds of pathogen associated molecular patternsand striking a cascade immune response in fish have been demonstrated. Miiuy croaker TLR13 significantly increased after infection with Vibrio anguillarum, which suggests that mmiTLR13 plays an important role in innate immunity. In this study, the role of miR-8159 was explored in regulating TLR13, which is involved in inflammatory responses in miiuy croakers. Bioinformatics was used to predict miR-8159, which has a direct negative regulatory effect on TLR13 in miiuy croaker. Afterward, the dual luciferase reporter assay containing miRNA mimics or inhibitors and pre-miR-8159 showed that miR-8159 was the direct negative regulator of TLR13 in miiuy croaker. Moreover, miR-8159 downregulated the expression of TLR13 in the transcription level. The expression of miR-8159 could be upregulated by V. anguillarum challenged miiuy croaker and LPS exposure macrophages. Thus, miR-8159 could be induced by V. anguillarum and may function as a negative regulator of TLR13 in the immune response of miiuy croakers.

The evolution and functional characterization of miiuy croaker interferon regulatory factor 9 involved in immune response

Interferon regulatory factors (IRFs) are transcription factors which play important roles in regulating the expression of type I interferons (IFNs) and IFN-stimulated genes. IRF9 is one of the IRF family gene members which belongs to the IRF4 subfamily. Mammalian IRF9 has been known to be involved in antiviral responses as the DNA sequence recognition subunit of IFN-stimulated gene factor 3 (ISGF3) complex. In fish, only a few studies investigated the characteristics of IRF9 and the role in IFN signaling. In this study, we identified the IRF9 gene from miiuy croaker (mmiIRF9) and studied its feature and function. Sequence analysis showed the similarity of mmiIRF9 and other fish IRF9 genes. Structural and syntenic analysis showed the conservatism in fish IRF9 genes. The result of expression analysis in normal tissues and infected tissues and macrophages showed that mmiIRF9 expressed in all tested normal tissues and up-regulated expression in liver, kidney and macrophages after stimulated with poly(I:C). Luciferase reporter assays demonstrated the mmiIRF9 can induced IFNα and IFNβ luciferase reporters and the cellular localization of mmiIRF9 was mainly distributed in the cytoplasm in Hela cells. Furthermore, the evolutionary analysis of IRF4 subfamily showed the IRF4 and IRF8 may be the most ancient and conservative genes in the evolution of this subfamily.

Two distinct CXC chemokine receptors (CXCR3 and CXCR4) from the big-belly seahorse Hippocampus abdominalis: Molecular perspectives and immune defensive role upon pathogenic stress

CXC chemokine receptor 3 (CXCR3) and 4 (CXCR4) are members of the seven transmembrane G protein coupled receptor family, involved in pivotal physiological functions. In this study, seahorse CXCR3 and CXCR4 (designated as HaCXCR3 and HaCXCR4) cDNA sequences were identified from the transcriptome library and subsequently molecularly characterized. HaCXCR3 and HaCXCR4 encoded 363 and 373 amino acid long polypeptides, respectively. The HaCXCR3 and HaCXCR4 deduced proteins have typical structural features of chemokine receptors, including seven transmembrane domains and a G protein coupled receptors family 1 profile with characteristic DRY motifs. Amino acid sequence comparison and phylogenetic analysis of these two CXC chemokine receptors revealed a close relationship to their corresponding teleost counterparts. Quantitative real time PCR analysis revealed that HaCXCR3 and HaCXCR4 were ubiquitously expressed in all the tested tissues, with highest expression levels in blood cells. The seahorse blood cells and kidney HaCXCR3 and HaCXCR4 mRNA expressions were differently modulated when challenged with Edwardsiella tarda, Streptococcus iniae, lipopolysaccharide, and polyinosinic:polycytidylic acid, confirming their involvement in post immune responses.

microRNA-145 regulates the RLR signaling pathway in miiuy croaker after poly(I:C) stimulation via targeting MDA5

MicroRNAs (miRNAs) are endogenous small non-coding RNAs that participate in diverse biological processes via degrading the target mRNAs or repressing translation. In this study, the regulation of miRNA to the RLR (RIG-I-like receptor) signaling pathway by degrading the target mRNAs was researched in miiuy croaker. MDA5, a microRNA-145-5p (miR-145-5p) putative target gene, was predicted by bioinformatics, and the target sites from the 3'untranslated region of MDA5 transcripts were confirmed using luciferase reporter assays. Pre-miR-145 was more effective in inhibiting MDA5 than miR-145-5p mimic, and the effect was dose- and time-dependent. The expression patterns of miR-145-5p and MDA5 were analyzed in liver and kidney from miiuy croaker. Results implied that miR-145-5p may function via degrading the MDA5 mRNAs, thereby regulating the RLR signaling pathway. Studies on miR-145-5p will enrich knowledge of its functions in immune response regulation in fish, as well as offer a basis for regulatory networks that are composed of numerous miRNAs.

Comparative genomic evidence for duplication of TLR1 subfamily and miiuy croaker TLR1 perceives LPS stimulation via MyD88 and TIRAP

Being indispensable pattern recognition receptors in innate immune responses in host protection, Toll-like receptors (TLRs) play an important role in pathogen recognition. Fish TLRs exhibit high variety and distinct features, although little is known about their function on ligand recognition and signaling pathway in fish. This paper reports the evolutionary spectrum of the TLR1 subfamily (referred to as TLR1, TLR6, and TLR10) as determined using the comparative genomic approach. We hypothesized that the TLR1 subfamily underwent two rounds of gene duplication events; the first duplication occurred prior to the divergence of amphibians, and the second one occurred prior to the divergence of eutherians. To further study the function of fish TLR1, we identified miiuy croaker (Miichthys miiuy) TLR1 (mmiTLR1) and determined its potential ability to perceive Vibrio anguillarum and lipopolysaccharide stimulation. Data further suggested that mmiTLR1 is dependent on TIRAP and MyD88 for signal transmission. In addition, immunocytochemistry showed the speculative interaction between MyD88 and mmiTLR1 TIR domain. Overall, we systematically and comprehensively analyzed evolution of TLR1 subfamily and the function of mmiTLR1, which will provide the basis for future scientific research on fish TLRs.

Discovery of toll-like receptor 13 exists in the teleost fish: Miiuy croaker (Perciformes, Sciaenidae)

Toll-like receptors (TLRs) play an indispensable role in the immune response for pathogen recognition and triggering not only innate immunity but also adaptive immunity. Here we report the TLR13 homologue, one member of TLRs, in Perciformes (especially Sciaenidae). And we used the miiuy croaker as represented species for further functional experiments. Former study reported the TLR13 only expressed in murine, and we are the first to report the teleost TLR13 (mmiTLR13). MmiTLR13 expressed highly in immune defense related tissues, such as the liver, spleen, and kidney, and Vibrio anguillarum or poly(I:C) infection showed the immune response of mmiTLR13. Further luciferase reporter assays showed the ability for activation of ISRE luciferase reporter, but it failed to active NF-κB. And further gene silence by short hairpin RNA (shRNA) confirmed the results. Immunofluorescence of mmiTLR13 presents the cytoplasmic distribution in Hela cell. In addition, the Toll/interleukin 1 receptor (TIR) domain of mammal TLR5 exhibits high identity with TLR13, which indicated the high homology between TLR5 and TLR13. These findings will lay the fundamental cornerstone for further research of teleost TLR13 and expand the horizon for better understand the teleost TLRs system.

Changes in selective pressures associated with human population expansion may explain metabolic and immune related pathways enriched for signatures of positive selection

Background

The study of local adaptation processes is a very important research topic in the field of population genomics. There is a particular interest in the study of human populations because they underwent a process of rapid spatial expansion and faced important environmental changes that translated into changes in selective pressures. New mutations may have been selected for in the new environment and previously existing genetic variants may have become detrimental. Immune related genes may have been released from the selective pressure exerted by pathogens in the ancestral environment and new variants may have been positively selected due to pathogens present in the newly colonized habitat. Also, variants that had a selective advantage in past environments may have become deleterious in the modern world due to external stimuli including climatic, dietary and behavioral changes, which could explain the high prevalence of some polygenic diseases such as diabetes and obesity.

Results

We performed an enrichment analysis to identify gene sets enriched for signals of positive selection in humans. We used two genome scan methods, XPCLR and iHS to detect selection using a dense coverage of SNP markers combined with two gene set enrichment approaches. We identified immune related gene sets that could be involved in the protection against pathogens especially in the African population. We also identified the glycolysis & gluconeogenesis gene set, related to metabolism, which supports the thrifty genotype hypothesis invoked to explain the current high prevalence of diseases such as diabetes and obesity. Extending our analysis to the gene level, we found signals for 23 candidate genes linked to metabolic syndrome, 13 of which are new candidates for positive selection.

Conclusions

Our study provides a list of genes and gene sets associated with immunity and metabolic syndrome that are enriched for signals of positive selection in three human populations (Europeans, Africans and Asians). Our results highlight differences in the relative importance of pathogens as drivers of local adaptation in different continents and provide new insights into the evolution and high incidence of metabolic syndrome in modern human populations.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2783-2) contains supplementary material, which is available to authorized users.

Identification and functional characterization of miiuy croaker IRF3 as an inducible protein involved regulation of IFN response

IFN regulatory factor (IRF) 3 as an important member of IRF family, is required for the host antiviral response. In mammals, IRF3 is known to be a critical player in regulating the transcription of IFN and IFN-stimulated genes (ISGs). However, only a few studies investigated the characteristics of IRF3 genes in fish. In this study, IRF3 from miiuy croaker was identified and characterized in bioinformatics and functions. Miiuy croaker IRF3 had conserved DBD, IAD and SRD domains with other vertebrates IRF3 genes, also miiuy croaker IRF3 had relatively conserved gene synteny and gene structures with other fish IRF3 genes. Evolutionary analysis showed IRF3 genes in mammals underwent positive selection, while IRF3 in fish underwent purifying selection. Expression analysis showed miiuy croaker IRF3 was expressed in all tested tissues and up-regulated expressed in infected liver and kidney; and up-regulated expression of miiuy croaker IRF3 was observed in head kidney macrophages which stimulated with poly(I:C) indicating that miiuy croaker IRF3 participated in the immune response to defense against poly(I:C) infection. Furthermore, luciferase reporter assay showed that overexpression of miiuy croaker IRF3 can activate the production of ISRE and IFNα, suggesting that miiuy croaker IRF3 acted as transcription activators in immune responses and maybe activate IFN signaling pathway. Immunofluorescence assay showed miiuy craoker IRF3 was localized in the cytoplasm in Hela cells. Overall, we systematically and comprehensively analyzed the bioinformatics and functions of miiuy croaker IRF3, which provided further insights into the transcriptional regulation of IRF3 gene in fish and valuable information for the study of evolution of IRF3 genes.

The miiuy croaker microRNA transcriptome and microRNA regulation of RIG-I like receptor signaling pathway after poly(I:C) stimulation

MicroRNAs (miRNAs) as endogenous small non-coding RNAs play key regulatory roles in diverse biological processes via degrading the target mRNAs or inhibiting protein translation. Previously many researchers have reported the identification, characteristic of miRNAs and the interaction with its target gene. But, the study on the regulation of miRNAs to biological processes via regulatory the key signaling pathway was still limited. In order to comprehend the regulatory mechanism of miRNAs, two small RNA libraries from the spleen of miiuy croaker individuals with or without poly(I:C) infection were constructed. The 197 conserved miRNAs and 75 novel miRNAs were identified, and 14 conserved and 8 novel miRNAs appeared significant variations. Those differently expressed miRNAs relate to immune regulation of miiuy croaker. Furthermore, expressions of four differently expressed miRNAs were validated by qRT-PCR, and the result was consistent with sequencing data. The target genes of the differently expressed miRNAs in the two libraries were predicted, and some candidate target genes were involved in the RIG-I-like receptor (RLR) signaling pathway. The negative regulation of miRNAs to target genes were confirmed by comparing the expression pattern of miRNAs and their target genes. The results of regulating target genes were that firstly directly or indirectly activating the downstream signaling cascades and subsequent inducting the type I interferon, inflammatory cytokines and apoptosis. These studies could help us to deeper understand the roles of miRNAs played in the fish immune system, and provide a new way to investigate the defense mechanism of fish.

Molecular characterization of three IRF1 subfamily members reveals evolutionary significance of IRF11 in miiuy croaker

The interferon regulatory factors IRF1 and IRF2 of the IRF1 subfamily play essential roles in immune responses against viruses. IRF11 is a novel IRF gene of the IRF1 subfamily; IRF11 genes share almost the same evolutionary distance with IRF1 and IRF2 genes. However, the structure and characteristics of IRF11 gene in fish have been rarely reported. In our study, IRF1, IRF2 and IRF11 genes were identified and characterized from miiuy croaker genome. Results showed that the IRF1, IRF2 and IRF11 genes contain the same domains; each of these genes is composed of conserved gene organizations and characterized by gene synteny with the orthologous genes. Interestingly, IRF11 was likely found only in fish (but not specific to teleost fish). Evolutionary analysis results showed that IRF1 gene in mammals, IRF2 and IRF11 gene in fish underwent positive selection. IRF1, IRF2 and IRF11 were expressed in a wide range of miiuy croaker tissues. These genes also exhibited the same expression patterns after miiuy croaker was infected with poly(I:C). Therefore, our data enhanced our understanding of the functions and evolution of IRF11 in fish.

Transcriptome comparative analysis revealed poly(I:C) activated RIG-I/MDA5-mediated signaling pathway in miiuy croaker

Miiuy croker (Miichthys miiuy) as an important economical aquaculture species has challenged many more diseases caused by various pathogens recently. To better explore the immune response to virus, we have analyzed the transcriptome profiling of miiuy croaker challenged with poly(I:C) synthetic analog of virus dsRNA. We have obtained differentially expressed genes (DEGs) with up/down-relevant from comparison of the Ctrl and Poly transcriptome libraries. Through GO and KEGG enrichment analysis, immune-relevant DEGs whose expression are significantly rise or fall after challenged have been identified and classified. In order to detailedly analysis host immune response patterns for dsRNA virus, we have performed a map based on RIG-I/MDA5-mediated and TLR3-mediated signaling pathway which both induced type I IFNs response. In this pathway, both MDA5 and LGP2 are important RLRs in host surveillance against infection of dsRNA viruses and induce type I IFNs response which subsequently form a transcription factor complex ISGF3 that promote downstream genes referred to as ISGs to inhibits virus replication.

Characterization and evolutionary analysis of duplicated C7 in miiuy croaker

The complement system, as one of the most sophisticated innate immune system, plays an important role in defense against invading microorganisms. The complement component C7 participates in the cytolytic phase of complement activation through a series of polymerization reactions with other terminal complement components. In this study, we derived two C7 genes from the whole genome of miiuy croaker which were the consequence of the fish-specific genome duplication. Our data showed that miiuy croaker C7-1 and C7-2 genes shared same structure domains. The analysis of gene synteny showed that high degree conserved of synteny was retained between miiuy croaker and other teleosts, and miiuy croaker had a relatively closer relationship with fugu. The expression of C7-1 and C7-2 in miiuy croaker healthy tissues revealed that they were ubiquitously expressed in all ten tested tissues. Besides, the immune response of C7-1 and C7-2 were different in spleen with Vibrio anguillarum, Staphylococcus aureus, poly I:C and LPS at 24 h post-injection, respectively. Furthermore, the expression patterns of C7-1 and C7-2 were different in liver, spleen and kidney after infected with V. anguillarum at different time-point. Evolutionary analysis showed that all the ancestral lineages underwent positive selection except for the ancestral lineages of fish C7-2, indicated that the ancestral lineages of fish C7-1 genes undertook more pressures than C7-2 in defense against the invading microorganisms. Meanwhile, a series of maximum likelihood methods were used to explore the evolutionary patterns on extant vertebrates' C7 genes. Three and one positive selection sites were found in extant mammalian C7 genes and fish C7-2 genes, but no positive selection site was found in extant fishes C7-1 genes. The result showed that extant fish C7-2 genes undertook more pressures compared with C7-1. In conclusion, fish C7-1 and C7-2 gene underwent different evolutionary patterns.

Molecular characterization, genomic structure and expressional profiles of a CXC chemokine receptor 4 (CXCR4) from rock bream Oplegnathus fasciatus

The CXC chemokine receptor 4 (CXCR4) is the cognate receptor of the CXC chemokine ligand 12 (CXCL12) and plays a pivotal role under immune-pathophysiological conditions. In the current study, the CXCR4 homolog of Oplegnathus fasciatus (OfCXCR4) was sequenced and the mRNA expression levels were characterized. The genomic structure of the cloned OfCXCR4 coding region (2094 bp) revealed a bi-exonic element, where the open reading frame (ORF) appears split by a single intron. Analysis of the ORF (1134 bp) of OfCXCR4 revealed a predicted protein of 42.1 kDa with typical seven transmembrane (TM) domain architecture and several conserved structural features, including two cysteine residues forming a predicted disulfide bond, a characteristic CXC motif (containing CYC) and a G-protein-coupled receptor (GPCR) family 1 signature. Furthermore, based on comparative analysis, the structure OfCXCR4 appears well conserved at both the genomic DNA and the amino acid levels. Phylogenic analysis of OfCXCR4 revealed that the greatest homology was with its teleostean relatives. Expression studies showed ubiquitous OfCXCR4 transcription, mainly in immune organs, with the highest levels in the head kidney. Examination of OfCXCR4 transcriptional regulation post injection to different stimuli or pathogens revealed a significant modulation of mRNA expression as detected by reverse transcription-quantitative real-time PCR. Evidence of various transcription factor binding sites present in the 5'-flanking region of OfCXCR4 coupled with its observed regulated mRNA expression suggest that it may have an important role in immune surveillance in rock bream.

The CXC chemokine receptors of fish: Insights into CXCR evolution in the vertebrates

This article will review current knowledge on CXCR in fish, that represent three distinct vertebrate groups: Agnatha (jawless fishes), Chondrichthyes (cartilaginous fishes) and Osteichthyes (bony fishes). With the sequencing of many fish genomes, information on CXCR in these species in particular has expanded considerably. In mammals, 6 CXCRs have been described, and their homologues will be initially reviewed before considering a number of atypical CXCRs and a discussion of CXCR evolution.

Characterization of the duplicate L-SIGN and DC-SIGN genes in miiuy croaker and evolutionary analysis of L-SIGN in fishes

Dendritic cell-specific ICAM-3-grabbing non-integrin (DC-SIGN/CD209) and liver/lymph node-specific ICAM-grabbing non-integrin (L-SIGN/CD299) which are homologues of DC-SIGN are important members in C-type lectin receptors family as key molecules to recognize and eliminate pathogens in the innate immune system. DC-SIGN and L-SIGN have become hot topics in recent studies which both served as cell adhesion and phagocytic pathogen recognition receptors in mammals. However, there have been almost no studies of DC-SIGN and L-SIGN structure and characters in fish, only DC-SIGN in the zebrafish had been studied. In our study, we identified and characterized the full-length miiuy croaker (Miichthys miiuy) DC-SIGN (mmDC-SIGN) and L-SIGN (mmL-SIGN) genes. The sequence analysis results showed that mmDC-SIGN and mmL-SIGN have the same domains with other vertebrates except primates, and share some conserved motifs in CRD among all the vertebrates which play a crucial role in interacting with Ca(2+) and for recognizing mannose-containing motifs. Gene synteny of DC-SIGN and L-SIGN were analyzed for the first time and gene synteny of L-SIGN was conserved among the five fishes. Interestingly, one gene next to L-SIGN from gene synteny had high similarity with L-SIGN gene that was described as L-SIGN-like in fish species. While only one L-SIGN gene existed in other vertebrates, two L-SIGN in fish may be in consequence of the fish-specific genome duplication to adapt the specific environment. The evolutionary analysis showed that the ancestral lineages of L-SIGN gene in fishes experienced purifying selection and the current lineages of L-SIGN gene in fishes underwent positive selection, indicating that the ancestral lineages and current lineages of L-SIGN gene in fishes underwent different evolutionary patterns. Both mmDC-SIGN and mmL-SIGN were expressed in all tested tissues and ubiquitously up-regulated in infected liver, spleen and kidney at different sampling time points, indicating that the mmDC-SIGN and mmL-SIGN participated in the immune response to defense against bacteria infection.

Comparative genomic of the teleost cathepsin B and H and involvement in bacterial induced immunity of miiuy croaker

Cathepsins are a family of lysosomal proteases play different roles at physiological and pathological states and present in almost all animals as well as other organisms. Cathepsins B and H are both cysteine proteases of cathepsins. Cathepsin B and H have been studied playing parts in protein degradation/turnover, antigen presentation/processing and hormone maturation in mammals. However, little is known about the structures and functions of cathepsin B and H in teleosts. In the present study, we identified and characterized the full-length miiuy croaker (Miichthys miiuy) cathepsin B and H genes. The sequence analysis results showed that both cathepsin B and H contain the characteristics of papain family with a signal peptide, propeptide and mature peptide regions. The comparison of the genomic organizations and locations indicated the conserved synteny and mild evolution in the cathepsin B and H genes adjacent regions. In addition, the gene synteny analysis showed that miiuy croaker cathepsin B has a closer relationship to stickleback and fugu than to cave fish and zebrafish, and cathepsin H was most similar with the 2 subtype in tilapia and fugu. By phylogenetic analysis, miiuy croaker cathepsin B and H were all assigned to cysteine proteases, and with a close relationship to Salmo salar cathepsin B and Oplegnathus fasciatus cathepsin H, respectively. Quantitative real-time RT-PCR analysis results confirmed that cathepsin B and H genes expressed ubiquitously in all tested healthy tissues from miiuy croaker. Furthermore, up-regulated expression of the cathepsin B and H transcripts in liver, spleen and kidney after exposure upon Vibrio anguillarum suggested that they may play important roles in innate immune response and antigen processing of miiuy croaker.

Molecular cloning, characterization and gene expression of murrel CXC chemokine receptor 3a against sodium nitrite acute toxicity and microbial pathogens

CXCR3 is a CXC chemokine receptor 3 which binds to CXC ligand 4 (CXCL4), 9, 10 and 11. CXC chemokine receptor 3a (CXCR3a) is one of the splice variants of CXCR3. It plays crucial role in defense and other physiological processes. In this study, we report the molecular cloning, characterization and gene expression of CXCR3a from striped murrel Channa striatus (Cs). The full length CsCXCR3a cDNA sequence was obtained from the constructed cDNA library of striped murrel by cloning and sequencing using an internal sequencing primer. The full length sequence is 1425 nucleotides in length including an open reading frame of 1086 nucleotides which is encoded with a polypeptide of 361 amino acids (mol. wt. 40 kDa). CsCXCR3a domain analysis showed that the protein contains a G protein coupled receptor between 55 and 305 along with its family signature at 129-145. The transmembrane prediction analysis showed that CsCXCR3a protein contains 7 transmembrane helical regions at 34-65, 80-106, 113-146, 154-181, 208-242, 249-278 and 284-308. The 'DRY' motif from CsCXCR3a protein sequence at (140)Asp-(141)Arg-(142)Tyr which is responsible for G-protein binding is also highly conserved with CXCR3 from other species. Phylogenetic tree showed that the CXC chemokine receptors 3, 4, 5 and 6, each formed a separate clade, but 1 and 2 were clustered together, which may be due to the high similarity between these receptors. The predicted 3D structure revealed cysteine residues, which are responsible for 'CXC' motif at 116 and 198. The CsCXR3a transcript was found to be high in kidney, further its expression was up-regulated by sodium nitrite acute toxicity exposure, fungal, bacterial and poly I:C challenges. Overall, these results supported the active involvement of CsCXCR3a in inflammatory process of striped murrel during infection. However, further study is necessary to explore the striped murrel chemokine signaling pathways and their roles in defense system.

Sequence and expression analysis of rainbow trout CXCR2, CXCR3a and CXCR3b aids interpretation of lineage-specific conversion, loss and expansion of these receptors during vertebrate evolution

The chemokine receptors CXCR1-3 bind to 11 chemokines (CXCL1-11) that are clustered on the same chromosome in mammals but are largely missing in ray-finned fish. A second CXCR1/2, and a CXCR3a and CXCR3b gene have been cloned in rainbow trout. Analysis of CXCR1-R3 genes in lobe-finned fish, ray-finned fish and tetrapod genomes revealed that the teleostomian ancestor likely possessed loci containing both CXCR1 and CXCR2, and CXCR3a and CXCR3b. Based on this synteny analysis the first trout CXCR1/2 gene was renamed CXCR1, and the new gene CXCR2. The CXCR1/R2 locus was shown to have further expanded in ray-finned fish. In relation to CXCR3, mammals appear to have lost CXCR3b and birds both CXCR3a and CXCR3b during evolution. Trout CXCR1-R3 have distinct tissue expression patterns and are differentially modulated by PAMPs, proinflammatory cytokines and infections. They are highly expressed in macrophages and neutrophils, with CXCR1 and CXCR2 also expressed in B-cells.