MAVS of triploid hybrid of red crucian carp and allotetraploid possesses the improved antiviral activity compared with the counterparts of its parents

GSTP1 is a negative regulator of MAVS in the antiviral signaling against SVCV infection

Glutathione S-transferase P1 (GSTP1), the most ubiquitous member of the GST superfamily, plays vital roles in the detoxification, antioxidant defense, and modulation of inflammatory responses. However, limited studies have been conducted on the function of GSTP1 in antiviral innate immunity. In this study, we have cloned the homolog of GSTP1 in triploid hybrid crucian carp (3nGSTP1) and investigated its regulatory role in the interferon signaling pathway. The open reading frame of 3nGSTP1 is composed of 627 nucleotides, encoding 209 amino acids. In response to spring viremia of carp virus (SVCV) infection, the mRNA level of 3nGSTP1 was up-regulated in the liver, kidney, and caudal fin cell lines (3 nF C) of triploid fish. The knockdown of 3nGSTP1 in 3 nF C improved host cell's antiviral capacity and attenuated SVCV replication. Additionally, overexpression of 3nGSTP1 inhibited the activation of IFN promoters induced by SVCV infection, poly (I:C) stimulation, or the RLR signaling factors. The co-immunoprecipitation assays further revealed that 3nGSTP1 interacts with 3nMAVS. In addition, 3nGSTP1 dose-dependently inhibited 3nMAVS-mediated antiviral activity and reduced 3nMAVS protein level. Mechanistically, 3nGSTP1 promoted ubiquitin-proteasome degradation of MAVS by promoting its K48-linked polyubiquitination. To conclude, our results indicate that GSTP1 acts as a novel inhibitor of MAVS, which negatively regulates the IFN signaling.

hnRNPM suppressed IRF7-mediated IFN signaling in the antiviral innate immunity in triploid hybrid fish

Mammalian heterogeneous nuclear ribonucleoproteins M (hnRNPM) is a critical splicing regulatory protein that has been reported to negatively regulate the RLR signaling pathway by impairing the binding of RIG-I and MDA5 to viral RNA. To explore the role of hnRNPM in the antiviral innate immune response in teleost fish, the hnRNPM homologue of triploid fish (3nhnRNPM) has been cloned and identified in this paper. The CDS of 3nhnRNPM gene is composed of 2016 nucleotides and encodes 671 amino acids. 3nhnRNPM migrated around 71 kDa in immunoblotting assay and was mainly detected in the nucleus in nucleo-cytoplasmic separation assay and immunofluorescent staining test. When 3nhnRNPM and 3nIRF7 were co-expressed in EPC cells, 3nhnRNPM significantly reduced the 3nIRF7-induced interferon (IFN) promoter transcription. Correspondingly, the mRNA levels of the SVCV-M, -N, -P, and -G genes were noteworthily enhanced, but the transcription levels of epcIFNφ1, epcMx1, epcPKR, and epcISG15 were dramatically decreased. Additionally, the knockdown of 3nhnRNPM resulted in restricted SVCV replication and enhanced host cell antiviral activity. Furthermore, the association between 3nhnRNPM and 3nIRF7 has been identified by the co-immunoprecipitation assay. In addition, we found that 3nIRF7 was detained in the nucleus when co-expressed with 3nhnRNPM. To sum up, our data supported the conclusion that 3nhnRNPM suppressed 3nIRF7-mediated IFN signaling in the antiviral innate immunity.

Intervention of Dietary Protein Levels on Muscle Quality, Antioxidation, and Autophagy in the Muscles of Triploid Crucian Carp (Carassius carassius Triploid)

The aim of this study is to investigate the effect of dietary protein levels on flesh quality, oxidative stress, and autophagy status in the muscles of triploid crucian carp (Carassius carassius triploid), and the related molecular mechanisms. Six experimental diets with different protein levels (26%, 29%, 32%, 35%, 38%, 41%) were formulated. A total of 540 fish with an initial weight of 11.79 ± 0.09 g were randomly assigned to 18 cages and six treatments with three replicates of 30 fish each for 8 weeks feeding. It could be found that the whole-body ash content significantly increased in high protein level groups (p < 0.05). The 29% dietary protein level group exhibited the highest muscle moisture, although there was an inconspicuous decrease in the chewiness of the muscles when compared with the other groups. The dietary protein level influenced the content of free amino acids and nucleotides, especially the content of flavor amino acids, which exhibited an increasing tendency along with the increasing protein level, such as alanine and glutamic acid, while the flavor nucleotides showed different fluctuation trends. Moreover, the genes related to muscle development were shown to be influenced by the dietary protein level, especially the expression of MRF4, which was up-regulated with the increasing dietary protein levels. The 29% dietary protein level promoted the majority of analyzed muscle genes expression to the highest level when compared to other dietary levels, except the Myostain, whose expression reached its highest at 38% dietary protein levels. Furthermore, the effect of dietary protein levels on antioxidant signaling pathway genes were also examined. High protein levels would boost the expression of GSTα; GPX1 and GPX4α mRNA expression showed the highest level at the 32% dietary protein group. The increasing dietary protein level decreased both mRNA and protein expressions of Nrf2 by up-regulating Keap1. Autophagy-related gene expression levels reached the peak at 32% dietary protein level, as evidenced by a similar change in protein expression of FoxO1. In summary, muscle nutritional composition, antioxidative pathways, and autophagy levels were affected by the dietary protein levels. A total of 29-32% dietary protein level would be the appropriate level range to improve muscle quality and promote the antioxidant and autophagy capacity of triploid crucian carp muscles.

Heterosis of growth trait regulated by DNA methylation and miRNA in allotriploid fish

Background

Heterosis of growth traits in allotriploid fish has benefited the production of aquaculture for many years, yet its genetic and molecular basis has remained obscure. Now, an allotriploid complex, including two triploids and their diploid inbred parents, has provided an excellent model for investigating the potential regulatory mechanisms of heterosis.

Results

Here, we performed a series of analyses on DNA methylation modification and miRNA expression in combination with gene expression in the allotriploid complex. We first established a model of cis- and trans-regulation related to DNA methylation and miRNA in allotriploids. Then, comparative analyses showed that DNA methylation contributed to the emergence of a dosage compensation effect, which reduced gene expression levels in the triploid to the diploid state. We detected 31 genes regulated by DNA methylation in the subgenomes of the allotriploids. Finally, the patterns of coevolution between small RNAs and their homoeologous targets were classified and used to predict the regulation of miRNA expression in the allotriploids.

Conclusions

Our results uncovered the regulatory network between DNA methylation and miRNAs in allotriploids, which not only helps us understand the regulatory mechanisms of heterosis of growth traits but also benefits the study and application of epigenetics in aquaculture.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13072-022-00455-6.

Identification and comparative study of melanoma differentiation-associated gene 5 homologues of triploid hybrid fish and its parents

Sterile triploid fish (3n = 150), derived from the hybridization between red crucian carp (Carassius auratus red var., ♀, 2n = 100) and allotetraploid (♂, 4n = 200), exhibits the improved disease resistance compared with its parents, but the current knowledge of the immunity of triploid fish is limited. Here, we report the identification and characterization of melanoma differentiation-associated gene 5 (MDA5) homologues from red crucian carp, triploid fish and allotetraploid. In this study, one red crucian carp MDA5 transcript (2nMDA5), two triploid fish MDA5 transcripts (3nMDA5-a and 3nMDA5-b) and two allotetraploid fish MDA5 transcripts (4nMDA5-a and 4nMDA5-b) have been cloned and identified separately. Immunofluorescence staining assay displayed that these MDA5 proteins were cytoplasmic proteins. RT-qPCR assay showed that, in response to spring viremia of carp virus (SVCV) and poly (I:C) stimuli, the increase of 3nMDA5 mRNA level was obviously higher than those of 2nMDA5 and 4nMDA5. Interestingly, the reporter assay and plaque assay revealed collectively that 3nMDA5-b, a shorter splicing form of MDA5, exhibited the strongest IFN promoter-inducing ability and antiviral activity. Additionally, when co-expressed with 3nMAVS, 3nMDA5-b induced a considerably higher level of IFN promoter activation than 3nMDA5-a; and the interactions between 3nMAVS/3nMDA5-a and 3nMAVS/3nMDA5-b were verified by co-IP assay. Taken together, our findings support the conclusion that in triploid fish, 3nMDA5-b mediates a robust antiviral signaling in host innate immune response.

Enhanced Immune Response Improves Resistance to Cadmium Stress in Triploid Crucian Carp

Previous research has indicated that triploid crucian carp (3n fish) have preferential resistance to cadmium (Cd) compared to Carassius auratas red var. (2n fish). In this article, comparative research is further conducted between the 2n and 3n fish in terms of the immune response to Cd-induced stress. Exposure to 9 mg/L Cd for 96 h changed the hepatic function indexes remarkably in the 2n fish, but not in the 3n fish. In the serum of Cd-treated 2n fish, the levels of alanine amino transferase, aspartate aminotransferase, adenosine deaminase, and total bilirubin significantly increased, while the levels of total protein, albumin, lysozyme, and anti-superoxide anion radicals decreased demonstrating hepatotoxicity. By analysis of transcriptome profiles, many immune-related pathways were found to be involved in the response of 3n fish to the Cd-induced stress. Expression levels of the immune genes, including the interleukin genes, tumor necrosis factor super family member genes, chemokine gene, toll-like receptor gene, and inflammatory marker cyclooxygenase 2 gene were significantly enhanced in the hepatopancreas of the Cd-treated 3n fish. In contrast, the expression levels of these genes decreased in the 2n fish. This research provides a theoretical basis for polyploid fish breeding and is helpful for the ecological restoration of water due to pollution.

Comparative analyses of hypothalamus transcriptomes reveal fertility-, growth-, and immune-related genes and signal pathways in different ploidy cyprinid fish

Triploid crucian carp (TCC) is obtained by hybridization of female diploid red crucian carp (Carassius auratus red var., RCC) and male allotetraploid hybrids. In this study, high-throughput sequencing was used to conduct the transcriptome analysis of the female hypothalamus of diploid RCC, diploid common carp (Cyprinus carpio L., CC) and TCC. The key functional expression genes of the hypothalamus were obtained through functional gene annotation and differential gene expression screening. A total of 71.56 G data and 47,572 genes were obtained through sequencing and genome mapping, respectively. The Fuzzy Analysis Clustering assigned the differentially expressed genes (DEGs) into eight groups, two of which, overdominance expression (6005, 12.62%) and underdominance expression (3849, 8.09%) in TCC were further studied. KEGG enrichment analysis showed that the DEGs in overdominance were mainly enriched in four pathways. The expression of several fertility-related genes was lower levels in TCC, whereas the expression of several growth-related genes and immune-related genes was higher levels in TCC. Besides, 15 DEGs were verified by quantitative real-time PCR (qPCR). The present study can provide a reference for breeding sterility, fast-growth, and disease-resistant varieties by distant hybridization.

Cytosolic Sensors for Pathogenic Viral and Bacterial Nucleic Acids in Fish

Recognition of the non-self signature of invading pathogens is a crucial step for the initiation of the innate immune mechanisms of the host. The host response to viral and bacterial infection involves sets of pattern recognition receptors (PRRs), which bind evolutionarily conserved pathogen structures, known as pathogen-associated molecular patterns (PAMPs). Recent advances in the identification of different types of PRRs in teleost fish revealed a number of cytosolic sensors for recognition of viral and bacterial nucleic acids. These are DExD/H-box RNA helicases including a group of well-characterized retinoic acid inducible gene I (RIG-I)-like receptors (RLRs) and non-RLR DExD/H-box RNA helicases (e.g., DDX1, DDX3, DHX9, DDX21, DHX36 and DDX41) both involved in recognition of viral RNAs. Another group of PRRs includes cytosolic DNA sensors (CDSs), such as cGAS and LSm14A involved in recognition of viral and intracellular bacterial dsDNAs. Moreover, dsRNA-sensing protein kinase R (PKR), which has a role in antiviral immune responses in higher vertebrates, has been identified in fish. Additionally, fish possess a novel PKR-like protein kinase containing Z-DNA binding domain, known as PKZ. Here, we review the current knowledge concerning cytosolic sensors for recognition of viral and bacterial nucleic acids in teleosts.

Black carp TRAFD1 restrains MAVS-mediated antiviral signaling during the innate immune activation

TRAFD1 negatively regulates TLR and RLR signaling in human and mammal; however, its role in teleost fish remains unknown. In this paper, the TRAFD1 homologue has been cloned and characterized from black carp (Mylopharyngodon piceus). Black carp TRAFD1 (bcTRAFD1) consists of 567 amino acids and shows low similarity to that of mammalian TRAFD1, which has been identified as a cytosolic protein through immunofluorescence staining. When co-expressed with bcTRAFD1, the IFN promoter-inducing ability of black carp MAVS (bcMAVS) was obviously dampened in the luciferase reporter assay. Accordingly, bcMAVS-mediated antiviral activity against grass carp reovirus (GCRV) and spring viremia of carp virus (SVCV) was potently repressed by bcTRAFD1 in plaque assay. And the co-immunoprecipitation assay between bcTRAFD1 and bcMAVS has identified the association between these two molecules. Thus, our data supports the conclusion that bcTRAFD1 interacts with bcMAVS and negatively regulates bcMAVS-mediated antiviral signaling during the innate immune activation, which sheds a light on the regulation of MAVS in teleost.

Comparative analysis and gut bacterial community assemblages of grass carp and crucian carp in new lineages from the Dongting Lake area

Gut microbiota are known to play an important role in health and nutrition of the host and have been attracting an increasing attention. Farming of new lineages of grass carp and crucian carp has been developed rapidly as these species were found to outperform indigenous ones in terms of growth rate and susceptibility to diseases. Despite this rapid development, no studies have addressed the characteristics of their gut microbiota as a potential factor responsible for the improved characteristics. To reveal whether microbiomes of the new lineages are different from indigenous ones, and therefore could be responsible for improved growth features, intestinal microbiota from the new lineages were subjected to high-throughput sequencing. While the phyla Firmicutes, Fusobacteria and Proteobacteria were representing the core bacterial communities that comprised more than 75% in all fish intestinal samples, significant differences were found in the microbial community composition of the new linages versus indigenous fish populations, suggesting the possibility that results in the advantages of enhanced disease resistance and rapid growth for the new fish lineages. Bacterial composition was similar between herbivorous and omnivorous fish. The relative abundance of Bacteroidetes and Actinobacteria was significantly higher in omnivores compared to that of herbivores, whereas Cetobacterium_sp. was abundant in herbivores. We also found that the gut microbiota of freshwater fish in the Dongting lake area was distinct from those of other areas. Network graphs showed the reduced overall connectivity of gut bacteria in indigenous fish, whereas the bacteria of the new fish lineage groups showed hubs with more node degree. A phylogenetic investigation of communities by reconstruction of unobserved states inferred function profile showed several metabolic processes were more active in the new lineages compared to indigenous fish. Our findings suggest that differences in gut bacterial community composition may be an important factor contributing to the rapid growth and high disease resistance of the new fish lineages.