Proteomic map of the differentially expressed proteins in the skin of Ctenopharyngodon idella against Aeromonas hydrophila infection.

The skin mucus of fish is an important part of the innate immune system, which is poorly understood at the proteomic level. The study established a complete map of the proteins in the skin mucus of Ctenopharangdon idella (C. idella) and discussed the Differentially Expressed Proteins (DEPs) after Aeromonas hydrophila (A. hydrophila) infection. Using Label Free Liquid Chromatography-Mass Spectrometry (LC-MS/MS) analysis, a total of 126 proteins were identified as differentially expressed, 89 proteins of which were upregulated, and 37 proteins were downregulated. Functional annotations of DEPs showed that the upregulated proteins in the skin mucus of the treated group were mostly associated with complement system and cytoskeleton proteins, whereas downregulated proteins were associated with metabolism. The key upregulated immune proteins were transferrin variant C, lysozyme g, annexin A11, 26S proteasome non-ATPase regulatory subunit 8, hypothetical protein ROHU_000884, 60S ribosomal L7a, calpain-2 catalytic subunit-like protein, calpain-9-like protein, complement component C9, complement C3, cathepsin S, cathepsin Z, 14 kDa apolipo, heat shock protein and intelectin, whereas, leukocyte elastase inhibitor, annexin A11, C-factor-like protein, biotinidase isoform X1 and epidermal growth factor receptor substrate 15-like were the downregulated proteins. Moreover, we for the first-time report proteins such as coactosin, lamin-B2 and kelch 12, which were never reported in fish. Our study directly pointing out the possible immunological biomarkers in the skin mucus of C. idella after A. hydrophila treatment. Each of the protein we report in this study could be used as base to establish their mechanism of action during bacterial infection that may contribute to the strategies against bacterial prevention and control in fishes.

Proteomic profile of epidermal mucus from Labeo rohita reveals differentially abundant proteins after Aeromonas hydrophila infection.

We report the proteomic profile of Epidermal Mucus (EM) from Labeo rohita and identified the differentially abundant proteins (DAPs) against Aeromonas hydrophila infection through label-free liquid chromatography-mass spectrometry (LC-MS/MS). Using discovery-based proteomics, a total of 2039 proteins were quantified in nontreated group and 1,328 proteins in the treated group, of which 114 were identified as DAPs in both the groups. Of the 114 DAPs, 68 proteins were upregulated and 46 proteins were downregulated in the treated group compared to nontreated group. Functional annotations of these DAPs shows their association with metabolism, cellular process, molecular process, cytoskeletal, stress, and particularly immune system. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis and Fisher's exact test between the two groups shows that most of the proteins were immune-related, which were significantly associated with the proteasome, phagosome, and Salmonella infection pathways. Overall, this study shows a basic and primary way for further functional research of the involvement of vitellogenin 2, alpha-2-macroglobulin-like protein, toll-like receptors (TLR-13), calpain, keratin-like proteins, and heat shock proteins against bacterial infection. Nonetheless, this first-ever comprehensive report of a proteomic sketch of EM from L. rohita after A. hydrophila infection provides systematic protein information to broadly understand the biological role of fish EM against bacterial infection.

Bactericidal role of epidermal mucus of freshwater fish treated with Aeromonas hydrophila.

This study explored the bactericidal role of the epidermal mucus (EM) of five freshwater Cyprinid fish species namely Ctenopharyngodon idella, Labeo rohita, Catla catla, Hypophthalmichthys molitrix, and Cirrhinus mrigala after treatment with Aeromonas hydrophila. Extracts of EM (crude and acidic) of each species showed bactericidal activity against various Gram -ve (Pseudomonas aeruginosa, Escherichia coli, Aeromonas hydrophila, Edwardsiella tarda, Salmonella enterica, Klebsiella pneumonia, Serratia marcescens, and Enterobacter cloacae) and Gram +ve (Bacillus wiedmannii and Staphylococcus aureus) bacteria compared with standard antibiotics (Fosfomycin). The zone of inhibition (ZOI) was measured in millimetres against antibiotics (Fosfomycin). Variations in bactericidal activity of EM were observed against bacteria from the same and different fish species. The acidic extract was more effective than the crude extract and showed significantly higher ZOI values against various bacteria and Fosfomycin antibiotics. This result shows that fish EM may perform an important role in fish defence against bacteria. Therefore, this study may hint towards the substitution of synthetic antibiotics with fish EM that may be used as a novel 'bactericidal' in aquaculture as well as in humans against bacterial infections.

Variations in the Behaviour, Survival, Haematology, and Biochemistry of Ctenopharyngodon idella (Grass Carp) After Exposure to Commercial Grade Atrazine.

The current study assessed the harmful effects of Atrazine (ATZ) herbicide on haematology and biochemistry of the freshwater fish Ctenopharyngodon idella, a commercially significant fish in Pakistan. C. idella (13 ± 8.4 cm; 132 ± 5.6 g) was exposed to graded levels of ATZ, and its 96-hour LC50 value at 25°C was calculated to be 150.5 µl/L. After exposure to ATZ, fish displayed rapid movements, a loss of balance in position and equilibrium, anxious swimming patterns, colour changes, and increased mucous production. The MCHC, MCH, RBCs, and Hb in C. idella decreased significantly (P < 0.05), whereas the MCV, Ht, and WBCs were significantly increased (P < 0.05). At different time intervals (24, 48, 72, and 96 h) following ATZ administration (50, 100, 150, and 200 µl/L), biochemical analysis significantly decreased (P < 0.05) triglyceride, total protein, cholesterol, and albumin levels, whereas glucose levels significantly increased (P < 0.05). We concluded that ATZ is toxic to C. idella, altering their haematology and blood biochemistry even after only a brief exposure.

Complete genome sequence analysis of Edwardsiella tarda SC002 from hatchlings of Siamese crocodile.

Edwardsiella tarda is a Gram-negative, facultative anaerobic rod-shaped bacterium and the causative agent of the systemic disease "Edwardsiellosis". It is commonly prevalent in aquatic organisms with subsequent economic loss and hence has attracted increasing attention from researchers. In this study, we investigated the complete genome sequence of a highly virulent isolate Edwardsiella tarda SC002 isolated from hatchlings of the Siamese crocodile. The genome of SC002 consisted of one circular chromosome of length 3,662,469 bp with a 57.29% G+C content and four novel plasmids. A total of 3,734 protein-coding genes, 12 genomic islands (GIs), 7 prophages, 48 interspersed repeat sequences, 248 tandem repeat sequences, a CRISPR component with a total length of 175 bp, and 171 ncRNAs (tRNA = 106, sRNA = 37, and rRNA = 28) were predicted. In addition, the coding genes of assembled genome were successfully annotated against eight general databases (NR = 3,618/3,734, COG = 2,947/3,734, KEGG = 3,485/3,734, SWISS-PROT = 2,787/3,734, GO = 2,648/3,734, Pfam = 2,648/3,734, CAZy = 130/3,734, and TCDB = 637/3,734) and four pathogenicity-related databases (ARDB = 11/3,734, CARD = 142/3,734, PHI = 538/3,734, and VFDB = 315/3,734). Pan-genome and comparative genome analyses of the complete sequenced genomes confirmed their evolutionary relationships. The present study confirmed that E. tarda SC002 is a potential pathogen bearing a bulk amount of antibiotic resistance, virulence, and pathogenic genes and its open pan-genome may enhance its host range in the future.

First Record of Ichthyofauna from Gomal Zam Dam, District South Waziristan, Khyber Pakhtunkhwa, Pakistan.

The present study reports the fish fauna of Gomal Zam Dam at three different sites from October 2018 to July 2019. The total sampled fish belong to 18 species, 15 genera, 5 families, and 4 orders. Fourteen species belong to family Cyprinidae, which was the most abundant, while one species belong to each family Mastacembelidae, Channidae, Siluridae, and Sisoridae. The prominent species were Labeo dyochielus (18.6%), Barilius vagra (16.5%), and Barilius pakistanicus (13.8%), while the rare species were Tor zhobensis, Wallago attu, Hyphophthalmicthys molitrix, Ctenophyrngodon idella, and Bagarius bagarius each one forming (0.1%). Species were rich in spring with ideal temperature, followed by summer, whereas species abundance was high in summer with high temperature and minimum abundance was recorded in autumn. In conclusion, the Gomal Zam Dam is a favorable reservoir for the fish particularly for family Cyprinidae. This present study will provide useful information about the diversity of fish fauna of Gomal Zam Dam that could be used in systematic fisheries management and conservation of the country.

Reactive Oxygen Species Accumulation Strongly Allied with Genetic Male Sterility Convertible to Cytoplasmic Male Sterility in Kenaf.

Male sterility (MS) plays a key role in the hybrid breed production of plants. Researchers have focused on the association between genetic male sterility (GMS) and cytoplasmic male sterility (CMS) in kenaf. In this study, P9BS (a natural GMS mutant of the kenaf line P9B) and male plants of P9B were used as parents in multiple backcross generations to produce P9SA, a CMS line with stable sterility, to explore the molecular mechanisms of the association between GMS and CMS. The anthers of the maintainer (P9B), GMS (P9BS), and CMS (P9SA) lines were compared through phenotypic, cell morphological, physiological, biochemical observations, and transcriptome analysis. Premature degradation of the tapetum was observed at the mononuclear stage in P9BS and P9SA, which also had lower activity of reactive oxygen species (ROS) scavenging enzymes compared with P9B. Many coexpressed differentially expressed genes were related to ROS balance, including ATP synthase, electron chain transfer, and ROS scavenging processes were upregulated in P9B. CMS plants had a higher ROS accumulation than GMS plants. The MDA content in P9SA was 3.2 times that of P9BS, and therefore, a higher degree of abortion occurred in P9SA, which may indicate that the conversion between CMS and GMS is related to intracellular ROS accumulation. Our study adds new insights into the natural transformation of GMS and CMS in plants in general and kenaf in particular.

Heavy Metals Assessment in Water, Sediments, Algae and Two Fish Species from River Swat, Pakistan.

The heavy metals were studied in water, sediments, algae, and various tissues of Glyptosternon reticulatum and Cyprinus carpio from River Swat, Pakistan, using flame atomic absorption spectrophotometer. The Zn, Cu, Pb and Ni were higher in water at sewage site compared to upstream and downstream sites. In sediments, the Ni and Cd were not detected whereas Cu, Pb and Zn were higher at downstream followed by sewage and upstream sites. The Ni and Zn in algae were higher at upstream and sewage sites compared to downstream site whereas Pb and Cd were higher at upstream site compared to sewage and downstream sites and Cu was found same at all the three sites. The heavy metals (Zn > Cu > Pb and Ni) in tissues (liver > gills > skin > muscles) of G. reticulatum was higher than in C. carpio. This study recommends the proper monitoring of River Swat in order to save its water and inhabitant aquatic life.

Growth and Metabolic Response of Chinese Perch to Different Dietary Protein-to-Energy Ratios in Artificial Diets.

The effect of dietary nutrients on novel farm species has always garnered wide research and economic interest. Chinese perch, an economically important carnivorous fish, accepts an artificial diet after taming, so it is essential to evaluate and optimize the nutritional and metabolic demands of this species. However, little is known about the effect of an artificial diet on the growth and metabolism of Chinese perch. Therefore, the present study evaluated the growth and metabolic responses of Chinese perch to experimental diets with different dietary protein/energy (P/E) ratios. Five isoenergetic diets (18 kJ/g) with graded levels of P/E ratios of 30.58, 33.22, 35.90, 38.6, and 41.35 mg/kJ (named A, B, C, D, and E) were formulated. A total of 225 Chinese perch (64.89 ± 0.28 g) were divided into five groups (triplicate tanks for each group), distributed into 15 (350 L) fiberglass tanks, and fed twice a day at 4% of fish wet body weight with the respective P/E ratio diets for 10 weeks. Compared with the other groups, Chinese perch in Group C showed significantly improved growth performance, weight gain (WG), specific growth rate (SGR), viscerosomatic index (VSI), hepatosomatic index (HSI), intraperitoneal fat (IPF), feed utilization, feed intake (FI), feed conversion ratio (FCR), protein efficiency ratio (PER), protein retention efficiency (PRE), energy retention efficiency (ERE), and feed efficiency (FE) as well as whole-body, muscle, and liver composition. Chinese perch in Group A, on the other hand, had the lowest growth performance, feed utilization, and body composition compared with the other groups. The activities of nitrogen metabolism-related enzymes (alanine aminotransferase (ALT), aspartate aminotransferase (AST) glutamate dehydrogenase (GDH), and adenosine 5'-monophosphate deaminase (AMPD)) as well as the mRNA expression of the GDH and AMPD genes were significantly lower than those in the other groups. Similarly, the expression of NPY and AgRp were significantly higher in Group C compared with the other groups. However, the gene expression of CART and POMC was not affected by the dietary P/E ratios. In Group A, the expression of mTOR, S6K, and 4EBP1 was significantly lower and that of AMPK, LKB1, and eEF2 was significantly higher when compared with the other groups. Biochemical analysis of blood showed that ALT, AST, total protein (TP), alkaline phosphatase (ALP), glucose (GLU), blood urea nitrogen (BUN), and triglyceride (TG) levels were also affected by the dietary P/E ratio. From our results, we concluded that Chinese perch growth performance and nutrient metabolism were significantly affected by the P/E ratio of the artificial diet. Second-order polynomial regression analysis revealed that Chinese perch growth performance was optimal at a P/E ratio of 37.98 in the artificial diet.

The RAG2 gene of yellow catfish (Tachysurus fulvidraco) and its immune response against Edwardsiella ictaluri infection.

Recombination-activating gene 2 (rag 2) allies with recombination-activating gene 1 (rag 1) and regulates the V(D)J recombination of immunoglobulin (Ig) and T-cell receptor (TCR) genes. Being a key player in the adaptive immune response of vertebrates, functional characterization of rag 2 from yellow catfish is beneficial for understanding the biological response towards the pathogens. In this report, we have cloned and characterized the rag 2 gene of yellow catfish, and a particular pattern of expression was analysed in the major tissues of yellow catfish. The results showed that the open reading frame (ORF) of yellow catfish rag 2 was 1596 bp in length, which encodes a peptide of 531 amino acids. The multiple sequence alignment and phylogenetic analysis of rag 2 of yellow catfish with other species showed the conserved regions and the classical taxonomic evolution among the different vertebrate species. The qRT-PCR and Western blot results revealed that rag 2 transcripts and proteins were present in various tissues of yellow catfish with relatively high expression in the tissues of the thymus, head-kidney, and spleen. The systematic distribution analysis of the rag 2 expression by immunohistochemistry (IHC) using the rabbit polyclonal antibody, exposed relatively high expression in head kidney, spleen and thymus tissues after infected with Edwardsiella ictaluri. Moreover, the temporal expression of rag 2 and pro-inflammatory cytokines (IL-1ß and TNF-α) were significantly upregulated at different time points in the specific lymphoid tissues of yellow catfish following E. ictaluri infection. Our findings suggest that rag 2 potentially exhibited the immunological response in primary lymphoid tissues of yellow catfish against bacterial infection. This study will provide an essential source about rag 2 gene and its relationship with the inflammatory cytokines during infection.

Transcriptomic analysis of differentially expressed genes and related pathways in Harmonia axyridis after sulfoxaflor exposure.

Harmonia axyridis (Pallas) is a major biological control agent that is indirectly threatened by sulfoxaflor insecticide applications targeting pests in agro-ecosystems. However, the genome-wide response of H. axyridis to sulfoxaflor remains largely unknown. Here, we used high-throughput RNA-seq technology to characterize the variation in the transcriptomic profile of second-instar H. axyridis larvae after exposure to sulfoxaflor. Two libraries were generated, with 50,702,976 and 47,005,096 clean reads for the sulfoxaflor treatment and control, respectively; these were grouped into 112,497 transcripts and 52,229 unigenes, of which 33,820 and 25,175 unigenes were respectively matched to proteins in the NCBI (Nr) and Swiss-Prot databases. From these unigenes, 794 significant differentially expressed genes (DEGs) consisting of 446 up- and 348 down-regulated genes, namely P450s, GSTs, USTs, ESTs, and others, were identified between the sulfoxaflor-treated and control groups. Furthermore, these DEGs were involved in several KEGG pathways including drug metabolism and metabolism of xenobiotic pathways. For transcriptome validation, 10 specifically expressed genes were selected and verified by quantitative real-time PCR analysis. Together, these results demonstrated that sulfoxaflor induces notable variation in the transcriptome profile and pathways of H. axyridis, which establishes a basis for further molecular investigations.

Isolation and functional identification of three cuticle protein genes during metamorphosis of the beet armyworm, Spodoptera exigua.

The beet armyworm, Spodoptera exigua (Hubner), is one of the major crop pests and is a target for current pest control approaches using insecticides. In this study three cuticular protein genes CPG316, CPG860 and CPG4855 have been cloned from 0 h pupal integument of S. exigua through race PCR Strategy. The deduced amino acid sequences were found to contain the RR-2 consensus region of other insect cuticular proteins and construct phylogenetic trees for each protein. Using quantitative RT-PCR, the developmental expression of the three genes through several larval and the early pupal stages was studied. All three genes contribute to the endocuticle although CPG316 may have a different role from the other two genes. All three newly isolated genes were analyzed and their functions were determined by using direct injection of the dsRNA into early 5th instar larvae. All genes are expressed in the larvae and early pupae but in different patterns. Furthermore, phenotypic results show that these genes have differing effects on the development of cuticle, its flexibility and a big role in metamorphosis in both larval and pupal stages.

Transcriptomic analysis reveals differentially expressed genes and a unique apoptosis pathway in channel catfish ovary cells after infection with the channel catfish virus.

The channel catfish virus (CCV) can cause lethal hemorrhagic infection in juvenile channel catfish, thereby resulting in a huge economic loss to the fish industry. The genome of the CCV has been fully sequenced, and its prevalence is well documented. However, less is known about the molecular mechanisms and pathogenesis of the CCV. Herein, the channel catfish ovary cells (CCO) were infected with CCV and their transcriptomic sketches were analyzed using an RNA sequencing technique. In total, 72,686,438 clean reads were obtained from 73,231,128 sequence reads, which were further grouped into 747,168 contigs. These contigs were assembled into 49,119 unigenes, of which 20,912 and 18,333 unigenes were found in Nr and SwissProt databases and matched 15,911 and 14,625 distinctive proteins, respectively. From these, 3641 differentially expressed genes (DEGs), comprising 260 up-regulated and 3381 down-regulated genes, were found compared with the control (non-infected) cells. For verification, 16 DEGs were analyzed using qRT-PCR. The analysis of the DEGs and their related cellular signaling pathways revealed a substantial number of DEGs that were involved in the apoptosis pathway induced by CCV infection. The apoptosis pathways were further elucidated using standard apoptosis assays. The results showed that CCV could induce extrinsic apoptosis pathway (instead of a mitochondrial intrinsic apoptosis pathway) in CCO cells. This study helps our understanding of the pathogenesis of CCV and contributes to the prevention of CCV infection in channel catfish.

Potential role of cyclophilin A in regulating cytokine secretion.

Cyclophilin A (CypA), a peptidylprolyl cis-trans isomerase, is a ubiquitous and multifunctional protein. In addition to its role as a host-cell receptor for cyclosporine A, CypA has diverse functions in inflammatory conditions and diseases. CypA secreted in response to inflammatory stimuli binds to the cell surface via its receptor CD147 and induces secretion of various inflammatory cytokines. However, silencing and inhibition of either CypA or CD147 inhibits inflammatory cytokine expression and inflammation. This report reviews the literature related to the mechanism of CypA-dependent cytokine secretion and discusses this factor as a possible therapeutic target in inflammatory diseases.

Potential contributions of heat shock proteins and related genes in sexual differentiation in yellow catfish (Pelteobagrus fulvidraco).

Sex determination and differentiation in ectotherms are very complicated affairs and usually affected by both genetic and environmental factors. Because of their temperature-sensitive expression, heat shock proteins (HSPs) are good candidates for temperature-dependent sex determination (TSD). Similar to most thermosensitive fish species, the male to female ratio increases with temperature in yellow catfish (Pelteobagrus fulvidraco). Yellow catfish is also a type of sexual size dimorphic fish, and the male individuals grow much faster than females of the same age. Therefore, research of sex differentiation in yellow catfish is important in aquiculture. In this attempt, a total of seven HSPs and related genes were identified from transcriptomes of yellow catfish by 454 pyrosequencing and Solexa sequencing that we did previously, including five genes with complete open reading frame (ORF). Phylogenetically, all these genes were compared with their counterparts from other vertebrates. All these genes were sex-biased expressed in gonads. Hspa5, Hip, and Cdc37 were expressed more highly in ovary than in testis, whereas Hsp90α, Hspb2, Hspb8, and Hspbp1 were expressed more highly in testis than in ovary. Additionally, the expression of these genes was assessed after 17α-methyltestosterone (MT) and 17α-ethinylestradiol (EE2) treatment, respectively. Our result showed that working as co-chaperones, these HSPs and related genes may regulate sex steroid receptor activities to influence gonad development in yellow catfish. Our work would help in the understanding of the mechanism of sexual differentiation in teleosts.

Updates in understanding the role of cyclophilin A in leukocyte chemotaxis.

Cyclophilin A (CypA), a well-recognized receptor for anti-inflammatory drug cyclosporine A (CsA) is a ubiquitous and multifunctional protein. Beside the diverse intracellular functions, CypA is secreted against inflammatory stimuli, where it activates and attracts leukocytes via CD147 to the stimulus site. Interestingly, it synergizes with other factors to induce leukocyte migration in different animals. However, the silencing and inhibition of CypA or CD147 inhibits leukocytes chemotaxis and inflammation. This review focuses on the advances made in understanding the mechanism of CypA-dependent leukocytes chemotaxis and hence, recognition of this factor as a possible therapeutic target in inflammatory diseases.

Cyclophilin A: A Key Factor in Virus Replication and Potential Target for Anti-viral Therapy.

Cyclophilin A (CypA) is a key member of immunophilins that has peptidyl-prolyl cis/trans isomerase (PPIase) activity. Besides acting as a cellular receptor for immunosuppressive drug cyclosporine A (CsA), CypA is involved in various cellular activities. CypA has an important role in viral infection which either facilitates or inhibits their replication. Inhibition of CypA via inhibitors is useful for overcoming several viral infections, indicating that CypA is an attractive target for anti-viral therapy. Collectively, these facts demonstrate the critical roles of CypA in mediating or inhibiting viral infections, suggesting that CypA can be an attractive cellular target for the development of anti-viral therapy.

Leucine mediates autophagosome-lysosome fusion and improves sperm motility by activating the PI3K/Akt pathway.

Amino acid supplementation is an efficient and effective strategy to increase sperm quality. In our research, a comparative study was conducted to screen free amino acids to improve sperm motility, and we found that leucine was the most efficient one. Leucine treatment increases sperm motility depending on the activation of PI3K/Akt signaling pathway, while the chemical inhibitor of PI3K/Akt signal could reduce the amount of pAkt activated by leucine treatment. Moreover, leucine treatment improved the expression of P62 and LC3-II, substantially suppressed the autophagy process in zebrafish testis. In vitro studies showed that leucine could reduce the fusion of autophagosome and lysosome that was indicated by the co-localization of EGFP-LC3 and lysosome marker. Two chemical modulators of autophagy, such as LY294002 (the inhibitor of PI3K/Akt signal) and chloroquine were administered to investigate the process of autophagy on zebrafish sperm motility. LY294002 inhibited autophagosome formation to reduced sperm motility, while chloroquine inhibited the fusion of autophagosome and lysosome to improve sperm motility. Our data suggest that short-term treatment with leucine could increase zebrafish sperm motility by affecting the autophagy and inhibiting the fusion of autophagosome and lysosomes, depending on the activation of PI3K/Akt signaling pathway.

Chemotactic Activity of Cyclophilin A in the Skin Mucus of Yellow Catfish (Pelteobagrus fulvidraco) and Its Active Site for Chemotaxis.

Fish skin mucus is a dynamic barrier for invading pathogens with a variety of anti-microbial enzymes, including cyclophilin A (CypA), a multi-functional protein with peptidyl-prolyl cis/trans isomerase (PPIase) activity. Beside various other immunological functions, CypA induces leucocytes migration in vitro in teleost. In the current study, we have discovered several novel immune-relevant proteins in yellow catfish skin mucus by mass spectrometry (MS). The CypA present among them was further detected by Western blot. Moreover, the CypA present in the skin mucus displayed strong chemotactic activity for yellow catfish leucocytes. Interestingly, asparagine (like arginine in mammals) at position 69 was the critical site in yellow catfish CypA involved in leucocyte attraction. These novel efforts do not only highlight the enzymatic texture of skin mucus, but signify CypA to be targeted for anti-inflammatory therapeutics.

Identification and Characterization of MicroRNAs in Snakehead Fish Cell Line upon Snakehead Fish Vesiculovirus Infection.

MicroRNAs (miRNAs) play important roles in mediating multiple biological processes in eukaryotes and are being increasingly studied to evaluate their roles associated with cellular changes following viral infection. Snakehead fish Vesiculovirus (SHVV) has caused mass mortality in snakehead fish during the past few years. To identify specific miRNAs involved in SHVV infection, we performed microRNA deep sequencing on a snakehead fish cell line (SSN-1) with or without SHVV infection. A total of 205 known miRNAs were identified when they were aligned with the known zebrafish miRNAs, and nine novel miRNAs were identified using MiRDeep2 software. Eighteen and 143 of the 205 known miRNAs were differentially expressed at three and 24 h post-infection (poi), respectively. From the differentially-expressed miRNAs, five were randomly selected to validate their expression profiles using quantitative reverse transcription polymerase chain reaction (qRT-PCR), and their expression profiles were consistent with the microRNA sequencing results. In addition, the target gene prediction of the SHVV genome was performed for the differentially-expressed host miRNAs, and a total of 10 and 58 differentially-expressed miRNAs were predicted to bind to the SHVV genome at three and 24 h poi, respectively. The effects of three selected miRNAs (miR-130-5p, miR-214 and miR-216b) on SHVV multiplication were evaluated using their mimics and inhibitors via qRT-PCR and Western blotting. The results showed that all three miRNAs were able to inhibit the multiplication of SHVV; whereas the mechanisms underlying the SHVV multiplication inhibited by the specific miRNAs need to be further characterized in the future.