Proteomic analysis of epithelioma papulosum cyprini cells infected with spring viremia of carp virus

Comparative Analysis of mRNA, microRNA of Transcriptome, and Proteomics on CIK Cells Responses to GCRV and Aeromonas hydrophila

Grass Carp Reovirus (GCRV) and Aeromonas hydrophila (Ah) are the causative agents of haemorrhagic disease in grass carp. This study aimed to investigate the molecular mechanisms and immune responses at the miRNA, mRNA, and protein levels in grass carp kidney cells (CIK) infected by Grass Carp Reovirus (GCRV, NV) and Aeromonas hydrophilus (Bacteria, NB) to gain insight into their pathogenesis. Within 48 h of infection with Grass Carp Reovirus (GCRV), 99 differentially expressed microRNA (DEMs), 2132 differentially expressed genes (DEGs), and 627 differentially expressed proteins (DEPs) were identified by sequencing; a total of 92 DEMs, 3162 DEGs, and 712 DEPs were identified within 48 h of infection with Aeromonas hydrophila. It is worth noting that most of the DEGs in the NV group were primarily involved in cellular processes, while most of the DEGs in the NB group were associated with metabolic pathways based on KEGG enrichment analysis. This study revealed that the mechanism of a grass carp haemorrhage caused by GCRV infection differs from that caused by the Aeromonas hydrophila infection. An important miRNA-mRNA-protein regulatory network was established based on comprehensive transcriptome and proteome analysis. Furthermore, 14 DEGs and 6 DEMs were randomly selected for the verification of RNA/small RNA-seq data by RT-qPCR. Our study not only contributes to the understanding of the pathogenesis of grass carp CIK cells infected with GCRV and Aeromonas hydrophila, but also serves as a significant reference value for other aquatic animal haemorrhagic diseases.

Infection of epithelioma papulosum cyprini (EPC) cells with spring viremia of carp virus (SVCV) induces autophagy and apoptosis through endoplasmic reticulum stress

Spring viremia of carp virus (SVCV) is a lethal freshwater pathogen of cyprinid fish that has caused significant economic losses to aquaculture. To reduce the economic losses caused by SVCV, its pathogenic mechanism needs to be studied more thoroughly. Here, we report for the first time that SVCV infection of Epithelioma papulosum cyprini (EPC) cells can induce cellular autophagy and apoptosis through endoplasmic reticulum stress. The presence of autophagic vesicles in infected EPC cells was shown by transmission electron microscopy. Quantitative fluorescence PCR and Western blot results showed that p62 mRNA expression was decreased, and the expression of Beclin1 and LC3 mRNA was increased. The p62 protein was decreased, and the Beclin1 protein and LC3 were increased in the endoplasmic reticulum stress activation state. To further clarify the mode of death of SVCV-infected EPC cells, we examined caspase3, caspase9, BCL-2, and Bax mRNA, which showed that they were all increased. Apoptosis of SVCV-infected cells increased upon activation of endoplasmic reticulum stress. Our results suggest that endoplasmic reticulum stress can regulate SVCV infection-induced autophagy and apoptosis. The results of this study provide theoretical data for the pathogenesis of SVCV and lay the foundation for future drug development and vaccine construction.

Proteomic Profiling of Zebrafish Challenged by Spring Viremia of Carp Virus Provides Insight into Skin Antiviral Response

Spring viremia of carp virus (SVCV) causes the skin hemorrhagic disease in cyprinid species, but its molecular mechanism of skin immune response remains unclear at the protein level. In the present study, the differential proteomics of the zebrafish (Danio rerio) skin in response to SVCV infection were examined by isobaric tags for relative and absolute quantitation and quantitative polymerase chain reaction (qPCR) assays. A total of 3999 proteins were identified, of which 320 and 181 proteins were differentially expressed at 24 and 96 h postinfection, respectively. The expression levels of 16 selected immune-related differentially expressed proteins (DEPs) were confirmed by qPCR analysis. Furthermore, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses revealed that DEPs were significantly associated with complement, inflammation, and antiviral response. The protein-protein interaction network of cytoskeleton-associated proteins, ATPase-related proteins, and parvalbumins from DEPs was shown to be involved in skin immune response. This is first report on the skin proteome profiling of zebrafish against SVCV infection, which will contribute to understand the molecular mechanism of local mucosal immunity in fish.

Proteomics for understanding pathogenesis, immune modulation and host pathogen interactions in aquaculture

Proteomic analyses techniques are considered strong tools for identifying and quantifying the protein contents in different organisms, organs and secretions. In fish biotechnology, the proteomic analyses have been used for wide range of applications such as identification of immune related proteins during infections and stresses. The proteomic approach has a significant role in understanding pathogen surviving strategies, host defence responses and subsequently, the fish pathogen interactions. Proteomic analyses were employed to highlight the virulence related proteins secreted by the pathogens to invade the fish host's defence barriers and to monitor the kinetics of protein contents of different fish organs in response to infections. The immune related proteins of fish and the virulence related proteins of pathogens are up or down regulated according to their functions in defence or pathogenesis. Therefore, the proteomic analyses are useful in understanding the virulence mechanisms of microorganisms and the fish pathogen interactions thereby supporting the development of new effective therapies. In this review, we focus and summarise the recent proteomic profiling studies exploring pathogen virulence activities and fish immune responses to stressors and infections.

Plasma proteomic analysis of zebrafish following spring viremia of carp virus infection

To better understand spring viremia of carp virus (SVCV) pathogenesis in zebrafish proteomic analysis was used to examine the plasma protein profile in SVCV-infected zebrafish. A total of 3062 proteins were identified. Of those 137, 63 and 31 proteins were enriched in blood samples harvested at 1, 2 and 5 days post SVCV infection, respectively. These altered host proteins were classified based on their biological function: 23 proteins under the response to stimulus term were identified. Interestingly, at the top of the up-regulated proteins during SVCV infection were the proteins of the vitellogenin family (Vtg) and the grass carp reovirus-induced gene (Gig) proteins. Real-time RT-PCR evaluation of samples from internal organs verified that SVCV infection induced vtg and gig2 gene expression already at day 1 post-infection. Western blot analysis revealed the presence of Vtg protein only in blood of SVCV-infected fish. This is the first proteomic study to reveal the involvement of Vtg proteins in adult fish response to viral challenge. It also highlights the role of Gig proteins as important factors in antiviral response in fish. This work provides valuable relevant insight into virus-host interaction and the identification of molecular markers of fish response to virus.

VER-155008 induced Hsp70 proteins expression in fish cell cultures while impeding replication of two RNA viruses

The heat-shock protein 70 (Hsp70) inhibitor, VER-155008 (VER), was explored as a potential antiviral agent for two RNA viruses important to fish aquaculture, viral hemorrhagic septicemia virus (VHSV) and infectious pancreatic necrosis virus (IPNV). Studies were done at a temperature of 14 °C, and with cell lines commonly used to propagate these viruses. These were respectively EPC from fathead minnow for VHSV and CHSE-214 from Chinook salmon embryo for IPNV. Additionally, both viruses were studied with the Atlantic salmon heart endothelial cell line ASHe. For both VHSV and IPNV, 25 μM VER impeded replication. This was evidenced by delays in the development of cytopathic effect (CPE) and the expression of viral proteins, N for VHSV and VP2 for IPNV, and by less production of viral RNA and of viral titre. As VER inhibits the activity of Hsp70 family members, these results suggest that VHSV and IPNV utilize one or more Hsp70s in their life cycles. Yet neither virus induced Hsp70. Surprisingly VER alone induced Hsp70, but whether this induction modulated VER's antiviral effects is unknown. Exploring this apparent paradox in the future should improve the usefulness of VER as an antiviral agent.

Synthesis and in vitro activities evaluation of arctigenin derivatives against spring viraemia of carp virus

Spring viraemia of carp virus (SVCV) is a viral fish pathogen causing high mortality in several carp species and other cultivated fish. However, robust anti-SVCV drugs currently are extremely scarce. For the purpose of seeking out anti-SVCV drugs, here a total of 35 arctigenin derivatives were designed, synthesized and evaluated for their anti-viral activities. By comparing the inhibitory concentration at half-maximal activity (IC₅₀) of the 15 screened candidate drugs (max inhibitory response surpassing 90%) in epithelioma papulosum cyprini (EPC) cells infected with SVCV, 2Q and 6 A were chosen for additional validation studies, with an IC₅₀ of 0.077 μg/mL and 0.095 μg/mL, respectively. Further experiments revealed that 2Q and 6 A could significantly decrease SVCV-induced apoptosis and have a protective effect on cell morphology at 48 and 72 h post-infection. Moreover, the reactive oxygen species (ROS) induced upon SVCV infection could be obviously inhibited by 2Q and 6 A, while SVCV-infected cells were clearly observed. On account of these findings, 2Q and 6 A could have a promising application for the treatment of infection of SVCV and provide a considerable reference for novel antivirals in aquaculture.

Combined transcriptomic/proteomic analysis of crucian carp Carassius auratus gibelio in cyprinid herpesvirus 2 infection

Cyprinid herpesvirus 2 (CyHV-2) is a pathogen of herpesviral hematopoietic necrosis disease of crucian carp. Our study aimed to investigate the molecular mechanisms and immune response at the mRNA and protein levels in head kidney during CyHV-2 infection. Three days after infection with CyHV-2, 7085 differentially expressed genes were identified by transcriptome sequencing, of which 3090 were up-regulated and 3995 were down-regulated. And 338 differentially expressed proteins including 277 up-regulated and 61 down-regulated were identified using tandem mass tag labeling followed by liquid chromatography tandem mass spectrometry. Notably, 128 differentially co-expressed genes at mRNA and protein levels (cDEGs) were reliably quantified, including 86 co-up-regulated and 42 co-down-regulated. In addition, 10 cDGEs in the above pathways were selected for qRT-PCR to confirm the validity of the transcriptome and proteome changes by showing that RIG-I, MDA5, LGP2, FAS, PKR and PKZ up-regulated and Integrin α, Integrin β2, NCF2 and NCF4 down-regulated. This indicated that after CyHV-2 infection, the herpes simplex infection pathway, RIG-I like receptor signaling pathway, necroptosis pathway and p53 signaling pathway were activated and the phagosome pathway was suppressed. Our findings reveal the pathogenesis and the host immune mechanism of CyHV-2 infection of crucian carp.

Highly efficient inhibition of spring viraemia of carp virus replication in vitro mediated by bavachin, a major constituent of psoralea corlifonia Lynn

As one of nine piscine viruses recognized by the International Office of Epizootics, spring viraemia of carp virus (SVCV) is an important pathogen bringing high mortality to cyprinids. Up to now, there is no approved therapy on SVCV, making them strong public health threat in aquaculture. In this study, the anti-SVCV activities of 12 plant crude extracts were investigated by using epithelioma papulosum cyprini (EPC) cells. Among these plants, Psoralea corylifolia Linn. showed the highest inhibition on SVCV replication, with an inhibitory percentage of 67.98%. Further studies demonstrated that bavachin (BVN), one of the major constituents of Psoralea corylifolia Linn., was also highly effective to SVCV infection. The half maximal inhibitory concentrations (IC₅₀) of BVN on SVCV glycoprotein and nucleoprotein expression were 0.46 (0.29-0.73) and 0.31 (0.13-0.55) mg/L, respectively. In addition, SVCV-induced apoptosis which may be negative to SVCV replication was inhibited by BVN. The apoptotic cells were decreased 21.42% for BVN compared with SVCV group. These results indicated that the inhibition of BVN on SVCV replication was, in some extent, via blocking SVCV induced apoptosis. Furthermore, cellular morphological damage induced by SVCV was also blocked by BVN treatment. Mechanistically, BVN did not affect SVCV infectivity and cannot be used for prevention of SVCV infection. Time-of-addition and viral binding assays revealed that BVN mainly inhibited the early events of SVCV replication but did not interfere with SVCV adsorption. In conclusion, BVN was considered to develop as a promising agent to treat SVCV infection.

Comparative transcriptome analysis of zebrafish (Danio rerio) brain and spleen infected with spring viremia of carp virus (SVCV)

Spring viremia of carp virus (SVCV) is the pathogen of spring viremia of carp (SVC) and often causes acute hemorrhagic symptoms in various kinds of cyprinids and induces serious environmental and economic losses. However, the molecular mechanisms of infection remain poorly understood, especially at the individual level. In this study, zebrafish was employed as the infection model to explore the pathogenesis of SVCV. 4 groups of zebrafish tissues were set and RNA sequencing (RNA-Seq) technology was employed to analyze the differentially expressed genes (DEGs) after SVCV-infection. A total of 360,971,498 clean reads were obtained from 12 samples, 382 DEGs in the brain and 926 DEGs in the spleen were identified. These DEGs were annotated into three ontologies after gene ontology (GO) enrichment analysis. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that these DEGs were primarily related to Influenza A pathway and Herpes simplex infection pathway in brain and Tuberculosis and Toxoplasmosis pathways in spleen, and all of these pathways may be involved in response to pathogen invasion. At the same time, 3' and 5' alternative splicing (AS) events were significantly up-regulated in the spleen. The transcriptome analysis results demonstrated changes and tissue-specific influences caused by SVCV in vivo, which provided us with more information to understand the complex relationships between SVCV and its host.

Evaluation on antiviral activity of coumarin derivatives against spring viraemia of carp virus in epithelioma papulosum cyprini cells

As one of the most serious pathogens in the freshwater aquatic environment, spring viraemia of carp virus (SVCV) induces a high mortality rate in several cyprinid fishes. In this study, we designed and synthesized a total of 44 coumarin derivatives to evaluate the anti-SVCV activity. By comparing the inhibitory concentration at half-maximal activity (IC₅₀), two imidazole coumarins (B4 and C2) were selected, with maximum inhibitory rates on SVCV more than 90%. Mechanistically, B4 or C2 did not affect viral adhesion and delivery from endosomes to the cytosol. Further, B4 and C2 could decline the apoptosis in SVCV-infected cells and the viral activated caspase-3, 8, 9 activities. Other results showed that SVCV induced the cytoskeletal structure to be a circumferential ring of microtubules near the nucleus, with occurring a disrupted microfilament organization. In comparison, cytoskeleton structure in drug-treated cells kept complete. In addition, the cellular microstructure in drug treatments showed no significant change; while SVCV-infected cells were seriously shrunk, and observed typical apoptotic features including cell shrinkage, volume reduction and cell blebbing. More importantly, B4 and C2 enhanced anti-oxidative enzyme gene expression and triggered the Nrf-2 pathway to keep balance of intracellular redox state. Therefore, the use of two imidazole coumarins (B4 and C2) could be a viable way of preventing and controlling SVCV infection.

Up-regulation of nuclear factor E2-related factor 2 (Nrf2) represses the replication of SVCV

Generation of reactive oxygen species (ROS) and failure to maintain an appropriate redox balance contribute to viral pathogenesis. Nuclear factor E2-related factor 2 (Nrf2) is an important transcription factor that plays a pivotal role in maintaining intracellular homoeostasis and coping with invasive pathogens by coordinately activating a series of cytoprotective genes. Previous studies indicated that the transcription and expression levels of Nrf2 were up-regulated in SVCV-infected EPC cells with the unknown mechanism(s). In this study, the interactions between the Nrf2-ARE signalling pathway and SVCV replication were investigated, which demonstrated that SVCV infection induced accumulation of ROS as well as protein carbonyl groups and 8-OHdG, accompanied by the up-regulation of Nrf2 and its downstream genes. At the same time, the activation of Nrf2 with D, l-sulforaphane (SFN) and CDDO-Me could repress the replication of SVCV, and knockdown of Nrf2 by siRNA could promote the replication of SVCV. Taken together, these observations indicate that the Nrf2-ARE signal pathway activates a passive defensive response upon SVCV infection. The conclusions presented here suggest that targeting the Nrf2 pathway has potential for combating SVCV infection.

Spring Viremia of Carp Virus N Protein Suppresses Fish IFNφ1 Production by Targeting the Mitochondrial Antiviral Signaling Protein

For a virus to replicate efficiently, it must try and inhibit host IFN expression because IFN is an important host defense at early stages after viral infection. For aquatic viruses, the mechanisms used to escape the hosts IFN system are still unclear. In this study, we show that the N protein of spring viremia of carp virus (SVCV) inhibits zebrafish IFNφ1 production by degrading the mitochondrial antiviral signaling protein (MAVS). First, the upregulation of IFNφ1 promoter activity stimulated by polyinosinic:polycytidylic acid, retinoic acid-inducible gene I (RIG-I) or MAVS was suppressed by the SVCV infection. However, the upregulation by the downstream factor of the RIG-I-like receptor signaling pathway, TANK-binding kinase 1, was not affected. Notably, at the protein level, MAVS decreased remarkably when cells were infected with SVCV. Second, consistent with the result of the SVCV infection, overexpression of the N protein of SVCV blocked the IFNφ1 transcription activated by MAVS and downregulated MAVS expression at the protein level but not at the mRNA level. Further analysis demonstrated that the N protein targeted MAVS for K48-linked ubiquitination, which promoted the degradation of MAVS. These data indicated that fish MAVS could be degraded by the N protein of SVCV through the ubiquitin-proteasome pathway. To our knowledge, this is the first article of a fish RIG-I-like receptor pathway interfered by an aquatic virus in an ubiquitin-proteasome manner, suggesting that immune evasion of a virus also exists in lower vertebrates.

Microarray analysis of gene expression in olive flounder liver infected with viral haemorrhagic septicaemia virus (VHSV)

The most fatal viral pathogen in olive flounder Paralichthys olivaceus, is viral hemorrhagic septicemia virus, which afflicts over 48 species of freshwater and marine fish. Here, we performed gene expression profiling on transcripts isolated from VHSV-infected olive flounder livers using a 13 K cDNA microarray chip. A total of 1832 and 1647 genes were upregulated and down-regulated over two-fold, respectively, after infection. A variety of immune-related genes showing significant changes in gene expression were identified in upregulated genes through gene ontology annotation. These genes were grouped into categories such as antibacterial peptide, antigen-recognition and adhesion molecules, apoptosis, cytokine-related pathway, immune system, stress response, and transcription factor and regulatory factors. To verify the cDNA microarray data, we performed quantitative real-time PCR, and the results were similar to the microarray data. In conclusion, these results may be useful for the identification of specific genes or for the diagnosis of VHSV infection in flounder.

Proteomic analysis of cellular protein expression profiles in response to grass carp reovirus infection

Grass carp (Ctenopharyngodon idella) hemorrhagic disease, caused by grass carp reovirus (GCRV), is emerging as a serious problem in grass carp aquaculture. To better understand the molecular responses to GCRV infection, two-dimensional electrophoresis (2-DE) and matrix-assisted laser desorption/ionization tandem mass spectroscopy were performed to investigate altered proteins in C. idella kidney (CIK) cells. Differentially expressed proteins in mock infected CIK cells and GCRV-infected CIK cells were compared. Twenty-three differentially expressed spots were identified (22 upregulated spots and 1 downregulated spot), which included cytoskeleton proteins, macromolecular biosynthesis-associated proteins, stress response proteins, signal transduction proteins, energy metabolism-associated proteins and ubiquitin proteasome pathway-associated proteins. Moreover, 10 of the corresponding genes of the differentially expressed proteins were quantified by real-time reverse transcription polymerase chain reaction to examine their transcriptional profiles. The T cell internal antigen 1 (TIA1) and Ras-GTPase-activating SH3-domain-binding protein1 (G3BP1) of the cellular stress granule pathway from grass carp C. idella (designated as CiTIA1 and CiG3BP1) were upregulated and downregulated during GCRV infection, respectively. The full-length cDNA of CiTIA1 was 2753 bp, with an open reading frame (ORF) of 1155bp, which encodes a putative 385-amino acid protein. The 2271 bp full-length cDNA of CiG3BP1 comprised an ORF of 1455 bp that encodes a putative 485-amino acid protein. Phylogenetic analysis revealed that the complete ORFs of CiTIA1 and CiG3BP1 were very similar to zebrafish and well-characterized mammalian homologs. The expressions of the cellular proteins CiTIA1 and CiG3BP1 in response to GCRV were validated by western blotting, which indicated that the GCRV should unlink TIA1 aggregation and stress granule formation. This study provides useful information on the proteomic and cellular stress granule pathway's responses to GCRV infection, which adds to our understanding of viral pathogenesis.

Proteomic identification and characterization of Ctenopharyngodon idella tumor necrosis factor receptor-associated protein 1 (CiTrap1): an anti-apoptosis factor upregulated by grass carp reovirus infection

Human tumor necrosis factor receptor-associated protein 1 (Trap1) is a mitochondrial protein identical to heat shock protein 75 (HSP75) that plays an important role in protecting cells from oxidative stress and apoptosis. In this study, grass carp (Ctenopharyngodon idella) tumor necrosis factor receptor-associated protein 1 (designated as CiTrap1) was identified through two-dimensional electrophoresis (2-DE) analysis and its pattern of expression was investigated in grass carp kidney (CIK) cells infected with grass carp reovirus (GCRV). The full length cDNA of CiTrap1 contained an opening reading frame of 2157 bp that encoded a peptide of 718 amino acids. Phylogenetic analyses indicated that the CiTrap1 shared 87% identity with its homologue from zebrafish (Danio rerio). The transcriptional level of CiTrap1 in CIK cells was upregulated post virus infection as well as poly (I: C) stimulation. Following virus infection, grass carp PTEN-induced putative kinase 1 (PINK1) and Sorcin, whose coding proteins interact with Trap1 in human, were simultaneously upregulated with CiTrap1. Typical characteristics of apoptosis were observed in CIK cells infected with GCRV by DAPI staining, DNA ladder electrophoresis, TUNEL assay and Annexin Ⅴ labeling. RNAi-mediated silencing of CiTrap1 in CIK cells resulted in the increased rate of virus-induced apoptotic cells. The results of this study suggest that CiTrap1 is involved in the host's innate immune response to viral infection possibly through protecting infected cells from apoptosis.

Tetracapsuloides bryosalmonae infection affects the expression of genes involved in cellular signal transduction and iron metabolism in the kidney of the brown trout Salmo trutta

Tetracapsuloides bryosalmonae is an enigmatic endoparasite which causes proliferative kidney disease in various species of salmonids in Europe and North America. The life cycle of the European strain of T. bryosalmonae generally completes in an invertebrate host freshwater bryozoan and vertebrate host brown trout (Salmo trutta) Linnaeus, 1758. Little is known about the gene expression in the kidney of brown trout during the developmental stages of T. bryosalmonae. In the present study, quantitative real-time PCR was applied to quantify the target genes of interest in the kidney of brown trout at different time points of T. bryosalmonae development. PCR primers specific for target genes were designed and optimized, and their gene expression levels were quantified in the cDNA kidney samples using SYBR Green Supermix. Expression of Rab GDP dissociation inhibitor beta, integral membrane protein 2B, NADH dehydrogenase 1 beta subcomplex subunit 6, and 26S protease regulatory subunit S10B were upregulated significantly in infected brown trout, while the expression of the ferritin M middle subunit was downregulated significantly. These results suggest that host genes involved in cellular signal transduction, proteasomal activities, including membrane transporters and cellular iron storage, are differentially upregulated or downregulated in the kidney of brown trout during parasite development. The gene expression pattern of infected renal tissue may support the development of intraluminal sporogonic stages of T. bryosalmonae in the renal tubular lumen of brown trout which may facilitate the release of viable parasite spores to transmit to the invertebrate host bryozoan.

Inhibition of spring viraemia of carp virus replication in an Epithelioma papulosum cyprini cell line by RNAi

Spring viraemia of carp virus (SVCV) is an aetiological agent of a serious disease affecting carp farms in Europe and is a member of the Rhabdoviridae family of viruses. The genome of SVCV codes for five proteins: nucleoprotein (N), phosphoprotein (P), matrix protein (M), glycoprotein (G) and RNA-dependent RNA polymerase (L). RNA-mediated interference (RNAi) by small interfering RNAs (siRNAs) is a powerful tool to inhibit gene transcription and is used to study genes important for viral replication. In previous studies regarding another member of Rhabdoviridae, siRNA inhibition of the rabies virus nucleoprotein gene provided in vitro and in vivo protection against rabies. In this study, synthetic siRNA molecules were designed to target SVCV-N and SVCV-P transcripts to inhibit SVCV replication and were tested in an epithelioma papulosum cyprini (EPC) cell line. Inhibition of gene transcription was measured by real-time quantitative reverse-transcription PCR (RT-qPCR). The efficacy of using siRNA for inhibition of viral replication was analysed by RT-qPCR measurement of a reporter gene (glycoprotein) expression and by virus endpoint titration. Inhibition of nucleoprotein and phosphoprotein gene expression by siRNA reduced SVCV replication. However, use of tandem siRNAs that target phosphoprotein and nucleoprotein worked best at reducing SVCV replication.

MicroRNA profile analysis of Epithelioma papulosum cyprini cell line before and after SVCV infection

MicroRNAs (miRNAs) play significant roles in regulating almost all of the biological processes in eukaryotes. An accumulating body of evidence shows that miRNAs are associated with cellular changes following viral infection. Spring viremia of carp virus (SVCV) is the pathogen of Spring viremia of carp (SVC), which results in heavy losses in the cultured common carp (Cyprinus carpio) industry in many countries. To study the involvement of miRNAs during SVCV infection, we adopted the Solexa sequencing technology to sequence small RNA libraries from the Epithelioma papulosum cyprini (EPC) cell line before and after infection with SVCV. In this study, a total of 161 conserved and 26 novel miRNAs were identified. Subsequently, the expression patterns of these miRNAs were compared between the uninfected (control library, M) and SVCV-infected (infection library, E) libraries. In addition, to verify the Solexa sequencing results, the expression patterns of 14 randomly selected miRNAs were validated by qRT-PCR. The targets of the significantly differentially expressed miRNAs were then predicted, and the miRNAs that could directly target the SVCV genome were also predicted. No miRNA encoded by SVCV itself was detected. To the best of our knowledge, this study presents the first miRNA profiling assessment in association with fish rhabdovirus infection, and the data presented lay a foundation for further investigations to determine the roles of miRNAs in regulating the molecular mechanism during SVCV infection.

Transcriptome analysis of epithelioma papulosum cyprini cells after SVCV infection

BACKGROUND

Spring viraemia of carp virus (SVCV) has been identified as the causative agent of spring viraemia of carp (SVC) and it has caused significant losses in the cultured common carp (Cyprinus carpio) industry. The molecular mechanisms that underlie the pathogenesis of the disease remain poorly understood. In this study, deep RNA sequencing was used to analyse the transcriptome and gene expression profile of EPC cells at progressive times after SVCV infection. This study addressed the complexity of virus-cell interactions and added knowledge that may help to understand SVCV.

RESULTS

A total of 33,849,764 clean data from 36,000,000 sequence reads, with a mean read length 100 bp, were obtained. These raw data were assembled into 88,772 contigs. Of these contigs, 19,642 and 25,966 had significant hits to the NR and Uniprot databases where they matched 17,642 and 13,351 unique protein accessions, respectively. At 24 h post SVCV infection (1.0 MOI), a total of 623 genes were differentially expressed in EPC cells compared to non-infected cells, including 288 up-regulated genes and 335 down-regulated genes. These regulated genes were primarily involved in pathways of apoptosis, oxidative stress and the interferon system, all of which may be involved in viral pathogenesis. In addition, 8 differentially expressed genes (DEGs) were validated by quantitative PCR.

CONCLUSIONS

Our findings demonstrate previously unrecognised changes in gene transcription that are associated with SVCV infection in vitro, and many potential cascades identified in the study clearly warrant further experimental investigation. Our data provide new clues to the mechanism of viral susceptibility in EPC cells.

Up-regulation of nuclear factor E2-related factor 2 upon SVCV infection

Nuclear factor E2 - related factor 2 (Nrf2) is a crucial transcription factor that regulates the basal and inducible expression of many antioxidant response element (ARE)-dependent genes, including heme oxygenase-1 (HO-1) and superoxide dismutase 1 (SOD1). The Nrf2/ARE pathway has been regarded as a critical switch in the initiation of cellular defence systems for surviving oxidative insults and viral infection. In this study, the Nrf2 gene of EPC cells, which is originally derived from Pimephales promelas, was cloned, and an investigation on the interactions between Nrf2 and spring viraemia of carp virus (SVCV) was performed. These results demonstrated that the virus facilitated the nuclear accumulation of Nrf2 and up-regulated its transcriptional and protein profiles in EPC cells. In addition, exogenous activation of Nrf2 conferred EPC cells with a higher cellular total antioxidant capacity via an increase in the expression of HO-1 and SOD1, but did not suppress the replication of SVCV.