Genomic structure of grass carp Mx2 and the association of its polymorphisms with susceptibility/resistance to grass carp reovirus

Comparative Transcriptomic Analysis Revealed Potential Differential Mechanisms of Grass Carp Reovirus Pathogenicity

Grass carp reovirus (GCRV), one of the most serious pathogens threatening grass carp (Ctenopharyngodon idella), can lead to grass carp hemorrhagic disease (GCHD). Currently, GCRV can be divided into three genotypes, but the comparison of their pathogenic mechanisms and the host responses remain unclear. In this study, we utilized the Ctenopharyngodon idella kidney (CIK) model infected with GCRV to conduct comparative studies on the three genotypes. We observed a cytopathic effect (CPE) in the GCRV-I and GCRV-III groups, whereas the GCRV-II group did not show any CPE. Moreover, a consistent trend in the mRNA expression levels of antiviral-related genes across all experimental groups of CIK cells was detected via qPCR and further explored through RNA-seq analysis. Importantly, GO/KEGG enrichment analysis showed that GCRV-I, -II, and -III could all activate the immune response in CIK cells, but GCRV-II induced more intense immune responses. Intriguingly, transcriptomic analysis revealed a widespread down-regulation of metabolism processes such as steroid biosynthesis, butanoate metabolism, and N-Glycan biosynthesis in infected CIK cells. Overall, our results reveal the CIK cells showed unique responses in immunity and metabolism in the three genotypes of GCRV infection. These results provide a theoretical basis for understanding the pathogenesis and prevention and control methods of GCRV.

The early response expression profiles of miRNA-mRNA in farmed yellow catfish (Pelteobagrus fulvidraco) challenged with Edwardsiella tarda infection

Edwardsiella tarda, the bacterial pathogen that causes ascites disease and red-head disease, poses a serious threat to yellow catfish (Pelteobagrus fulvidraco) aquaculture. In this study, the spleens of E. tarda-infected and non-infected yellow catfish were sequenced to obtain the microRNA (miRNA) and mRNA expression profiles. We obtained 657 differentially expressed (DE) miRNAs and 6867 DE mRNAs between two groups and annotated them using the KEGG database. In addition, the 43 negatively correlated miRNA-mRNA pairs were identified using integrated miRNA-mRNA analysis, which including immune-related miRNAs and target genes such as miR-144, miR-1260, miR-1388, miR-33, miR-338, miR-181b, miR-34c, miR-135 and CLEC4E, LITR, PIKfyve, NCF4, IL-12β, IP6K2, TNFRSF9, IL-4Rα, IRF2, Mx2. We verified 8 DE miRNAs pairs and 10 DE mRNAs by quantitative real-time PCR. Finally, the CLEC4E and Mx2 mRNAs were selected for further verification using in situ hybridization. Together, our results provide valuable information for further analyses of the mechanisms of yellow catfish defense against E. tarda infection.

SNP-based susceptibility-resistance association and mRNA expression regulation analyses of tlr7 to grass carp Ctenopharyngodon idella reovirus

Eleven single nucleotide polymorphisms (SNP) in Ctenopharyngodon idella toll-like receptor 7 (citlr7) gene, containing two in the 5'-flanking region, three within the single intron and six distributed in the coding sequence (CDS), were identified. A case-control study of 73 susceptible individuals and 67 resistant individuals was conducted to test the SNPs-based susceptibility-resistance association and mRNA expression of citlr7 to grass carp reovirus (GCRV), showing that both 820 A/G and 1726 A/G were significantly correlative sites in genotype (P < 0·05). Multifactor dimensionality reduction (MDR) analysis suggested the exertion of antiviral effects of 820 A/G might rely on SNPs interactions of citlr7 and C. idella toll-like receptor 8 (citlr8). Combining the mortality rate and citlr7 mRNA expression, it was suggested that 1726 GG-genotyped individuals might be more resistant than 1726 A/G genotyped individuals, indicating the selection on synonymous mutations in 1726 A/G might be susceptibility-resistance-type specific. In addition, haplotype analysis uncovered no significantly correlative haplotypes in citlr7. These findings may provide an in-depth insight for the further functional research of citlr7. The potential genetic markers identified may contribute to the molecular and transgenic breeding of C. idella.

Genomic structure, expression pattern and polymorphisms of GILT in golden pompano Trachinotus ovatus (Linnaeus 1758)

The interferon-g-inducible lysosomal thiol reductase (GILT) plays a significant character in the processing and presentation of MHC class II restricted antigen (Ag) by catalyzing disulfide bond reduction in mammals. To explore the function of GILT in the immune system of fish, we cloned a GILT gene homologue from Trachinotus ovatus, the full-length cDNA of GILT, which consisted of 2, 747 bp with a 771 bp open reading frame, encoding a protein of 256 amino acids. Moreover, similar to other species GILT gene, 7 exons and 6 introns were identified in T. ovatus, the deduced protein also possessed a representative characteristic of known GILT proteins. The result of real-time quantitative PCR showed that GILT mRNA was dramatically expressed in immune-associated tissues, such as spleen (p < 0.01) and kidney (p < 0.05). Bacterial challenge revealed that GILT mRNA level remarkably up-regulation in liver, spleen, kidney and intestine after induction with Photobacterium damsela. Furthermore, based on cloned sequences and genome BLAST, only one SNP site (ToGILT-S1-g.148C>G) was identified, and the allele C was significantly associated with high-susceptibility (HS) group, nevertheless, the allele G was dramatically associated with high-resistance (HR) group, indicating potential application for disease resistant breeding selection in T. ovatus.

A plasmid containing CpG ODN as vaccine adjuvant against grass carp reovirus in grass carp Ctenopharyngodon idella

CpG oligodeoxynucleotides (ODNs) are proved to have strong immune stimulatory activity. Plasmids containing CpG ODNs could be conveniently and low-costly used as vaccine adjuvant. However, they are different among various plasmids, motif repeats, species, etc. In the present study, plasmid pcDNA3.1 (+) containing five repetitions of CpG ODN 1670A named pcDNA3.1-1670A*5 with strong immunostimulation was screened out from twelve recombinant plasmids and three empty vectors by cell proliferation activity, interferon promoter activities and immune related gene expressions in CIK cells. It works through TLR9-mediated signaling pathway, triggering the immune related genes expression. Furthermore, the potentiality of pcDNA3.1-1670A*5 as adjuvant was tested in vivo. pcDNA3.1-1670A*5 was co-inoculated with inactivated GCRV vaccine on grass carp fingerlings. Immunoglobulins (IgM, IgD, IgZ), TLR9, IFNγ2, IFN1, TNF-α, Mx2 and VP4 were examined. Ultimately, pcDNA3.1-1670A*5 significantly enhanced the expressions of IgM in serum, head kidney and spleen, recognition receptor TLR9 as well as antiviral effector molecule Mx2, and inhibited GCRV proliferation in head kidney and spleen tissues. The present study explored the application and mechanism of plasmid containing CpG ODN as high-efficient adjuvant to promote efficiency of vaccine and control disease in grass carp, which will contribute to the development of new type CpG ODN adjuvant in aquaculture industry.

The polymorphism of chicken-type lysozyme gene in Japanese flounder (Paralichthys olivaceus) and its association with resistance/susceptibility to Listonella anguillarum

Lysozyme is a crucially spread hydrolase in organisms that can defend against bacterial infection in innate immunity. In this study, we successfully sequenced the coding region of chicken-type lysozyme gene (PoLysC) in Paralichthys olivaceus and identified nine single nucleotide polymorphisms (SNPs). We then amplified the 2500 bp promoter region of lysozyme and identified the eight sites of polymorphisms. All SNPs were genotyped between susceptible and resistance groups after Listonella anguillarum challenge. One of these SNP sites in the codon of PoLysC was genotyped and determined to be a significant marker by analyzing its distribution in the susceptible and resistant groups. As a nonsynonymous mutation, the frequency of 140G/C genotype in the resistant group was higher (67.74%) than that in the susceptible group (32.26%). The linkage between SNP140 and polymorphisms in the promoter region was also studied. Results revealed that the frequency of haplotype CC_-536/CC_-1200/GG₁₄₀ in the resistance group was significantly higher than that in the susceptible group. The quantitative expression of lysozyme gene in the resistant group was also higher than that in the susceptible group. This finding indicated that the linkage between polymorphism -536 and -1200 sites in promoter and SNP140 in codon sequence was associated with the resistance of P. olivaceus to L. anguillarum. All these results suggest that the mutations in promoter and coding region were related to changes in PoLysC for resisting L. anguillarum. The haplotype CC_-536/CC_-1200/GG₁₄₀ was a potential marker and can thus be applied to selective breeding for the disease resistance of P. olivaceus.

Molecular cloning and immune responsive expression of a ribonuclease III orthologue involved in RNA interference, dicer, in grass carp Ctenopharyngodon idella

In this study, the dicer gene (designated as cidicer) was identified and characterized from grass carp Ctenopharyngodon idella. The complementary DNA (cDNA) of cidicer contained an open reading frame (ORF) of 5646 nucleotides (nts) encoding a putative protein of 1881 amino acids (aa). The deduced Dicer protein contained all known functional domains identified in other organisms. Tissue tropism analysis indicated that cidicer is abundantly expressed in brain, gill, head kidney, liver, spleen, heart, muscle and intestine. In the C. idella kidney (CIK) cells, messenger RNA (mRNA) expression of cidicer was significantly up-regulated at 24 h (6·36-fold, P < 0·01) after grass carp reovirus (GCRV) infection, and its transcriptional expression level was also transiently induced to a high level (6·54-fold, P < 0·01) at 2 h post-stimulation of synthetic double-stranded polyinosinic-polycytidylic potassium salt [poly(I:C)]. In vivo analysis further showed that the expression of cidicer mRNA in the liver was induced to a significantly high level at 12 h (8·46-fold, P < 0·01), and then dropped to normal level at 72 h post-challenge with GCRV. The transcriptional expression pattern of cidicer in the spleen tissue was similar to that of liver tissue upon GCRV challenge. These results collectively implied that the identified cidicer was an inducible gene responding to viral infection both in vitro and in vivo, and the data would shed light on the interaction between RNA interference (RNAi) antiviral pathway and aquareovirus infection.

A new haplotype variability in complement C6 is marginally associated with resistance to Aeromonas hydrophila in grass carp

Aeromonas hydrophila, a widespread bacterium in the aquatic environment, causes haemorrhagic septicemia in fish. In the last decade, the disease has caused mass mortality and tremendous economic loss in cultured grass carp in the mainland China. The complement component C6 is a constituent of a biochemical cascade that serves as a major effector of the human innate and adaptor immunity, and eliminates infected cells. The objective of this study was to identify single nucleotide polymorphisms (SNPs) in the C6 gene and to assess their association with A. hydrophila resistance in grass carp. A resource population consisting of 186 susceptible and 191 resistant grass carp was constructed. The gcC6 genomic sequence is composed of 9292 bp, containing 18 exons and 17 introns. The promoter sequence of gcC6 gene contained several consensus sequences for hepatic-specific transcription factors. We sequenced a total of 9744 bp of the C6 gene from a diverse population of grass carp and identified 8 SNPs that were genotyped in the resource population. Statistical analysis revealed a lack of association between any individual SNPs and resistance to A. hydrophila in grass carp. The SNPs 1214G>A, 1380G>C, 2095A>C and 2167T>C were linked together (r(2) > 0.8). The haplotype GCCC generated with these four SNPs was associated marginally with resistance to A. hydrophila in grass carp. These findings suggest a lack of strong association of the C6 polymorphisms with the A. hydrophila resistance in grass carp.

Genomic sequence comparison, promoter activity, SNP detection of RIG-I gene and association with resistance/susceptibility to grass carp reovirus in grass carp (Ctenopharyngodon idella)

As an intracellular pattern recognition receptor (PRR), retinoic acid-inducible gene-I (RIG-I) is responsible for detection of nucleic acids from pathogens in infected cells and activation of type I interferon (IFN). In the present study, the 5'-flanking region, introns and single nucleotide polymorphisms (SNPs) of CiRIG-I (Ctenopharyngodon idella RIG-I) were identified and characterized. The genomic CiRIG-I was 12810 bp in length, consisted of an 1864 bp 5'-flank region whose promoter activity was confirmed, 15 exons and 14 introns. By pooled DNA sequencing, two SNPs were detected in the 5'-flanking region; 10 SNPs were discovered in introns; and one SNP was found in exons. After a challenge experiment, these SNPs were selected to analyze their association with the resistance/susceptibility of C. idella to grass carp reovirus (GCRV), using case-control study. Chi-square test was employed to assess the association. The result showed that -780 C/T, 4731 C/T, 4945 A/G, 8461 C/T, and haplotype 3428A-3432G were significantly associated with the phenotype (P<0.05). To confirm the correlation, another independent challenge experiment was performed, in which the cumulative mortality of -780 genotype CC, 4731 genotype CC and 4945 genotype AA were significantly lower than that of -780 genotype TT, 4731 genotype TT and 4945 genotype GG, respectively (P<0.05). In addition, the SNP-SNP interaction analysis revealed that there was no significant interaction among those SNPs (P>0.05). These significant SNPs and the haplotype might be potential genetic markers for the molecular selection of C. idella strains that are resistant to GCRV.

Lipopolysaccharide-induced TNF-α factor in grass carp (Ctenopharyngodon idella): evidence for its involvement in antiviral innate immunity

Lipopolysaccharide-induced TNF-α factor (LITAF), which participates in innate immune response and regulates TNF-α transcription, has been identified and characterized in various organisms. In a study to screen interacting cellular proteins with grass carp reovirus using yeast two-hybrid system, a grass carp homologue of LITAF was identified to bind the NS26 protein encoded by the S11 genomic fragment of Grass carp reovirus (GCRV). In this study, grass carp LPS-induced TNF-α factor gene (designated as CiLITAF) was cloned and sequenced from the cDNA library constructed for the yeast two-hybrid screening. The CiLITAF cDNA contained an open reading frame (ORF) of 483 bp encoding a polypeptide of 161 amino acids with an estimated molecular mass of 17.0 kDa. In CIK cells infected with GCRV or treated with poly (I:C), transiently stimulated transcription of CiLITAF mRNA was noticed at 8 h post infection or poly (I:C) treatment. Grass carp TNF-α (CiTNFα) transcriptional level was also transiently induced to a high level following the stimulation of CiLITAF in these in vitro tests. In vivo analysis further showed that, significantly up-regulated transcriptional expression of both CiLITAF and CiTNFα were detected in the spleen tissue as early as 48 h post challenge with GCRV. This study thus characterized CiLITAF as an inducible gene responding to viral infection.

Protective roles of grass carp Ctenopharyngodon idella Mx isoforms against grass carp reovirus

Background

Myxovirus resistance (Mx) proteins are crucial effectors of the innate antiviral response against a wide range of viruses, mediated by the type I interferon (IFN-I) signaling pathway. However, the antiviral activity of Mx proteins is diverse and complicated in different species.

Methodology/Principal Findings

In the current study, two novel Mx genes (CiMx1 and CiMx3) were identified in grass carp (Ctenopharyngodon idella). CiMx1 and CiMx3 proteins exhibit high sequence identity (92.1%), and low identity with CiMx2 (49.2% and 49.5%, respectively) from the GenBank database. The predicted three-dimensional (3D) structures are distinct among the three isoforms. mRNA instability motifs also display significant differences in the three genes. The spatial and temporal expression profiles of three C. idella Mx genes and the IFN-I gene were investigated by real-time fluorescence quantitative RT-PCR (qRT-PCR) following infection with grass carp reovirus (GCRV) in vivo and in vitro. The results demonstrated that all the four genes were implicated in the anti-GCRV immune response, that mRNA expression of Mx genes might be independent of IFN-I, and that CIK cells are suitable for antiviral studies. By comparing expression patterns following GCRV challenge or poly(I:C) treatment, it was observed that GCRV blocks mRNA expression of the four genes. To determine the functions of Mx genes, three CiMx cDNAs were cloned into expression vectors and utilized for transfection of CIK cells. The protection conferred by each recombinant CiMx protein against GCRV infection was evaluated. Antiviral activity against GCRV was demonstrated by reduced cytopathic effect, lower virus titer and lower levels of expressed viral transcripts. The transcription of IFN-I gene was also monitored.

Conclusions/Significance

The results indicate all three Mx genes can suppress replication of grass carp reovirus and over-expression of Mx genes mediate feedback inhibition of the IFN-I gene.

A 15 nucleotide deletion mutation in coding region of the RIG-I lowers grass carp (Ctenopharyngodon idella) resistance to grass carp reovirus

RIG-I (Retinoic acid-inducible gene I) is a pivotal receptor that detects numerous RNA and DNA viruses and plays crucial roles in the induction of type I interferons. In the present study, a deletion mutation in CiRIG-I (Ctenopharyngodon idella RIG-I) coding region was detected, its association with resistance/susceptibility to grass carp reovirus (GCRV) was examined, and possible mechanism was analyzed. A 15-bp deletion mutation was found, and the mutation results in a deletion of five amino acids. To investigate the genotypes and alleles, the relevant PCR products were electrophoresed on 2.5% agarose gel. Three genotypes and two alleles were discovered. The general allele was named as A and the deletion mutation allele was named as B. The deletion mutation cancels a predicted phosphorylation site and changes the secondary structure and the probability of peroxisomal targeting signal 1 in CiRIG-I. To explore the correlation between these genotypes and the resistance of grass carp to GCRV, a challenge experiment was carried out. The cumulative mortality in genotype AA (40.70%) and AB (52.73%) was significantly lower than that in genotype BB (71.43%) (P = 0.032). The result demonstrated that genotype AA and AB were resistant to GCRV, while genotype BB was susceptible. The 15-bp deletion mutation lowers the resistance of grass carp to GCRV. This result might provide a potential genetic marker for further investigation of selective breeding of resistant grass carp to GCRV.

Functional characterizations of RIG-I to GCRV and viral/bacterial PAMPs in grass carp Ctenopharyngodon idella

Background

RIG-I (retinoic acid inducible gene-I) is one of the key cytosolic pattern recognition receptors (PRRs) for detecting nucleotide pathogen associated molecular patterns (PAMPs) and mediating the induction of type I interferon and inflammatory cytokines in innate immune response. Though the mechanism is well characterized in mammals, the study of the accurate function of RIG-I in teleosts is still in its infancy.

Methodology/Principal Findings

To clarify the functional characterizations of RIG-I in grass carp Ctenopharyngodon idella (CiRIG-I), six representative overexpression plasmids were constructed and transfected into C. idella kidney (CIK) cell lines to obtain stably expressing recombinant proteins, respectively. A virus titer test and 96-well plate staining assay showed that all constructs exhibited the antiviral activity somewhat. The quantitative real-time RT-PCR (qRT-PCR) demonstrated that mRNA expressions of CiIPS-1, CiIFN-I and CiMx2 were regulated by not only virus (GCRV) or viral PAMP (poly(IC)) challenge but also bacterial PAMPs (LPS and PGN) stimulation in the steadily transfected cells. The results showed that the full-length CiRIG-I played a key role in RLR pathway. The repressor domain (RD) exerted an inhibitory function of the signaling channel under all utilized challenges. Caspase activation and recruitment domains (CARDs) showed a positive role in GCRV and poly(I:C) challenge. Helicase motifs were crucial for the signaling pathway upon LPS and PGN stimulation. Interestingly, ΔCARDs (CARDs deleted) showed postive modulation in RIG-I signal transduction.

Conclusions/Significance

The results provided some novel insights into RIG-I sensing with a strikingly broad regulation in teleosts, responding not only to the dsRNA virus or synthetic dsRNA but also bacterial PAMPs.

Identification and expression profiles of grass carp Ctenopharyngodon idella tlr7 in responses to double-stranded RNA and virus infection

The toll-like receptor 7 (tlr7) gene was identified and characterized from grass carp Ctenopharyngodon idella (designated as citlr7), and the messenger (m)RNA expression profiles were examined in vivo and in vitro. The citlr7 genomic sequence consists of 4276 nucleotides (nts), including two exons and one intron. The full length of citlr7 complementary (c)DNA sequence is 3354 nts with the longest open reading frame (ORF) of 3156 nts encoding a peptide of 1051 amino acids. citlr7 mRNA expression was high in spleen, skin and heart, and low in hepatopancreas, muscle, head kidney and trunk kidney in healthy fish. The expression of citlr7 was rapidly and significantly up-regulated at 6 h after grass carp reovirus (GCRV) injection (72·91 fold, P < 0·05), and recovered to the original level at 24 h post-injection in the spleen. The citlr7 transcript was rapidly and significantly down-regulated at the 6 h time point (0·32 fold, P < 0·05) and retrieved the normal level at 72 h post-injection in the hepatopancreas. The citlr7 transcripts were rapidly and significantly inhibited at 2 h post-GCRV infection in the C. idella kidney (CIK) cell line (0·62 fold, P < 0·05), and were rapidly and significantly elevated by the stimulation of the synthetic double-stranded RNA polyriboinosinic-polyribocytidylic acid sodium salt [poly(I:C)] in CIK in a dose and time-dependent manner (P < 0·05). The results imply that citlr7 is involved in the responses to double-stranded RNA and virus infection.