microRNA-19a as a negative regulator in TLR signaling pathway by direct targeting myeloid differentiation factor 88 in miiuy croaker

Regulatory roles of miRNA-530 in the post-transcriptional regulation of NF-κB signaling pathway through targeted modulation of IκBα in Sebastesschlegelii

MicroRNAs (miRNAs) are a crucial type of non-coding RNAs involved in post-transcriptional regulation. The playing essential regulatory roles in the NF-κB signaling pathway and modulate the host immune response to diverse pathogens by targeting IκBα. However, the regulatory mechanism of miRNAs in relation with IκBα in Sebastes schlegelii remains unclear. In our study, we identified two copies of IkBα gene in black rockfish (Sebastes schlegelii), namely IkBα1 and IkBα2. Moreover, we have discovered that miRNA-530 can activate the NF-κB signaling pathway by inhibiting the expression of IκBα, thereby inducing the inflammatory response. This project comprehensively investigated the interactive regulatory roles of miRNA-530 in the NF-κB signaling pathway at both cellular and in vivo levels, while also elucidating the regulatory relationships between miRNA-530 and IκBα. In conclusion, our research confirmed that miRNA-530 can target the 3'UTR region of IκBα, resulting in a decrease in the expression of IκBα at the post-transcriptional level and inhibiting its translation. The findings contribute to the understanding of the regulatory network of non-coding RNA in teleosts and its subsequent regulation of the NF-κB signaling pathway by miRNAs.

miR-144 affects the immune response and activation of inflammatory responses in Cynoglossus semilaevis by regulating the expression of CsMAPK6

MicroRNAs are increasingly recognized for their pivotal role in the immune system, yet the specific regulatory functions of fish-derived microRNAs remain largely unexplored. In this research, we discovered a novel miRNA, Cse-miR-144, in the Chinese tongue sole (Cynoglossus semilaevis), characterized by a 73-base pair precursor and a 21-nucleotide mature sequence. Our findings revealed that the expression of Cse-miR-144 was notably inhibited by various Vibrio species. Utilizing bioinformatics and dual-luciferase assay techniques, we established that the pro-inflammatory cytokine gene CsMAPK6 is a direct target of Cse-miR-144. Subsequent in vitro and in vivo western blotting analyses confirmed that Cse-miR-144 can effectively reduce the protein levels of CsMAPK6 post-transcriptionally. Moreover, CsMAPK6 is known to be involved in the activation of the Nuclear Factor kappa-light-chain-enhancer of activated B cells (NF-kB). Additional investigations using qPCR and ELISA demonstrated that suppression of Cse-miR-144 leads to an upsurge in the liver mRNA levels of various immune genes (including MYD88, TRAF6, NF-κB, TRAF2, TRAF3, and TNF), alongside a marked increase in the production and secretion of pro-inflammatory cytokines (IL-1β, IL-6, and IL-8) in the bloodstream of C. semilaevis. These findings collectively underscore the potential of Cse-miR-144 as a key inhibitor of CsMAPK and its crucial role in modulating the immune and inflammatory responses in teleost fish. Compared to the siRNA, miRNA is a better tool in controlling the expression of target gene with a lower cost.

TLR pathway signaling molecules in burbot (Lota lota): molecular characterization, basal expression, and their response to Poly(I:C)

Burbot (Lota lota), a fish species of economic and ecological significance found across northern hemisphere freshwater ecosystems, was the focus of this study. We characterized 19 Toll-like receptor (TLR) genes in burbot, tracing their expression patterns following pathogen exposure. TLR genes, crucial to the innate immune system, including TLR13-1/2/3, TLR2/2-2/2-3/2-4/2-5, and TLR22a/22b/22c/22d, were discovered to be tandemly repeated, signifying an evolution in the fish's immune system. Notably, different TLR subfamilies displayed tissue-specific expressions, with TLR1 primarily in spleen and head kidney, TLR13 in head kidney, trunk kidney, and heart, TLR22 in trunk kidney and liver, and TLR3 and TLR9 predominantly in spleen and head kidney, but also in trunk kidney. Further, we investigated the response of TLR genes in burbot to pathogen exposure using qRT-PCR. This involved measuring mRNA expressions of identified TLR genes in spleen and liver tissues after injecting Poly(I:C) to simulate a double-stranded RNA viral infection. The results revealed a time and tissue-specific expression pattern. Specifically, LoTLR3 reached peak expression in the spleen 12 h post-injection, declining thereafter, while TLR2 subfamily members only began expressing after 24 h. In the liver, activation of the TLR3-IRF7 and TLR3-IRF3 signaling pathways was noted. Integrating these results with transcriptomic data illuminated the pivotal role of TLR genes in the burbot's immune response. Such findings are vital in shaping future disease prevention and treatment strategies.

Identification of a novel fusion gene NLRC3-NLRP12 in miiuy croaker (Miichthys miiuy)

Fusion gene is a new gene formed by the fusion of all or part of the sequences of two genes, it is caused by chromosome translocation, middle deletion or chromosome inversion. Numerous studies in the past have continuously shown that gene fusions are tightly associated with the occurrence and development of various diseases, especially cancer. Many fusion genes have been identified in humans. However, few fusion genes have been identified in fish. In this study, a novel NLRC3-NLRP12 fusion gene was identified in the Miichthys miiuy (miiuy croaker) by quantitative real-time PCR (qRT-PCR), PCR, and Sanger sequencing. This fusion gene is fused by two genes related to NLRs (nucleotide binding domain and oligomerization domain like receptors). We found that the expression of the NLRC3-NLRP12 fusion gene was significantly upregulated after infection with Vibrio anguillarum (V. anguillarum) or stimulation with lipopolysaccharide (LPS). In addition, the NLRC3-NLRP12 fusion gene was strongly induced by V. anguillarum infection, peaking within the kidney and liver at 12 h post infection. Further functional experiments showed that overexpression of NLRC3-NLRP12 significantly inhibited nuclear factor kappa-B (NF-κB) activation. This study suggests that the newly discovered NLRC3-NLRP12 fusion genes may play an important role in innate immunity in miiuy croaker.

Non-coding RNAs targeting NF-κB pathways in aquatic animals: A review

Nuclear factor-kappa B (NF-κB) pathways have a close relationship with many diseases, especially in terms of the regulation of inflammation and the immune response. Non-coding RNAs (ncRNAs) are a heterogeneous subset of endogenous RNAs that directly affect cellular function in the absence of proteins or peptide products; these include microRNAs (miRNAs), long noncoding RNAs (lncRNAs), circular RNAs (circRNAs), etc. Studies on the roles of ncRNAs in targeting the NF-κB pathways in aquatic animals are scarce. A few research studies have confirmed detailed regulatory mechanisms among ncRNAs and the NF-κB pathways in aquatic animals. This comprehensive review is presented concerning ncRNAs targeting the NF-κB pathway in aquatic animals and provides new insights into NF-κB pathways regulatory mechanisms of aquatic animals. The review discusses new possibilities for developing non-coding-RNA-based antiviral applications in fisheries.

Functional characterization of four TIR domain-containing adaptors, MyD88, TRIF, MAL, and SARM in mandarin fish Siniperca chuatsi

Toll/interleukin-1 receptor (TIR) domain-containing adaptors, serve as pivotal signal transduction molecules in Toll-like receptor (TLR) signalling pathway to mediate downstream signalling cascades. In this study, four TIR-domain containing adaptors, MyD88, TRIF, MAL and SARM, were identified in mandarin fish Siniperca chuatsi, and they all contain TIR domains, of which MyD88 and SARM had high sequence homology with their vertebrate homologues. The expression analysis at mRNA level indicated that these genes were ubiquitously distributed in different tissues, being high in immune- and mucosa-related tissues such as head-kidney and intestine. The transcripts of these adaptor genes were up-regulated by poly(I:C) and LPS stimulation in isolated head-kidney lymphocytes (HKLs) of mandarin fish. Fluorescence microscopy revealed that all these molecules were localized in cytoplasm, and further investigations showed that the over-expression of MyD88, TRIF and MAL activated the NF-κB, ISRE or type Ι IFN promoters and inhibited SVCV replication, whereas their antiviral effects were significantly impaired when co-transfected with SARM. It was also confirmed by co-immunoprecipitation (Co-IP) that SARM interacts separately with MyD88, TRIF and MAL, and MAL interacts with MyD88. However, the regulatory mechanisms of these adaptors involved in signalling pathways of different TLRs should be of interest for further research.

Research progress on the regulation of nutrition and immunity by microRNAs in fish

MicroRNAs (miRNAs) are a class of highly conserved, endogenous non-coding single-stranded small RNA molecules with a length of 18-25 nucleotides. MiRNAs can negatively regulate the target gene through complementary pairing with the mRNA. It has been more than 20 years since the discovery of miRNA molecules, and many achievements have been made in fish research. This paper reviews the research progress in the regulation of fish nutrition and immunity by miRNAs in recent years. MiRNAs regulate the synthesis of long-chain polyunsaturated fatty acids, and are involved in the metabolism of glucose, lipids, as well as cholesterol in fish. Moreover, miRNAs play various roles in antibacterial and antiviral immunity of fish. They can promote the immune response of fish, but may also participate in the immune escape mechanism of bacteria or viruses. One important aspect of miRNAs regulation on fish immunity is mediated by targeting pattern recognition receptors and downstream signaling factors. Together, current results indicate that miRNAs are widely involved in the complex regulatory network of fish. Further studies on fish miRNAs may deepen our understanding of the regulatory network of fish nutrition and immunity, and have the potential to promote the development of microRNA-based products and detection reagents that can be applied in aquaculture industry.

IRF1 negatively regulates NF-κB signaling by targeting MyD88 for degradation in teleost fish

MyD88 is considered as one of the most crucial adaptors in TLR signaling pathway. MyD88 may be influential to interferon regulatory factors (IRFs), while the way that IRFs regulate MyD88 is not fully understood. In this study, we demonstrated that the member of IRF family named IRF1 in miiuy croaker played a role as a negative regulator of MyD88-mediated NF-κB signaling and promoted the degradation of MyD88. Firstly, we found the strong inhibitory effect of IRF1 on MyD88-mediated NF-κB signaling pathway. Secondly, we confirmed that IRF1 could enhance the degradation of MyD88, while the knockdown of IRF1 presented an opposite result. Furthermore, the DBD domain of IRF1 was necessary for the inhibition to MyD88. In addition, it could be found that IRF1 could promote MyD88 degradation through ubiquitin-proteasome pathway. Our findings suggest that miiuy croaker IRF1 negatively regulates the cellular response by targeting MyD88 for degradation, which provides new insights into the regulatory mechanism in teleost.

Molecular evolution and functional characterization of SOCS3a and SOCS3b in miiuy croaker (Miichthys miiuy)

The suppressor of cytokine signaling 3 (SOCS3), as a negative regulator in inferferon (IFN) signaling pathways in mammals, has a vital role in immune systems. However, studies on the function of SOCS3 in lower vertebrates are limited. In this study, we identified SOCS3a and fish-specific SOCS3b gene in miiuy croaker. Sequence analysis results showed that SOCS3a and SOCS3b were evolutionarily conservative in fish. Expression analysis indicated that miiuy croaker SOCS3a and SOCS3b (mmSOCS3a and mmSOCS3b) were expressed in all of the tested miiuy croaker tissues, thus revealing the potential ability to perceive poly (I:C) stimulation. Further functional experiments showed that mmSOCS3a and mmSOCS3b could inhibit the IFNγ- and IFNα-induced ISRE reporter activation, respectively. Accordingly, the investigation of mmSOCS3a and mmSOCS3b can provide insights into fish SOCS3 and a basis for future research on the SOCS family of fish immune systems.

DIGIRR as a member of the toll/IL-1R family negative regulates NF-κB signaling pathway in miiuy croaker

The double-Ig-IL-1R related molecule (DIGIRR) is a member of the TIR (Toll -Interleukin-1 receptor) superfamily and plays an important role in the immune system, it is also as a negative regulator of the IL-1 signaling pathway. In this study, we identified and characterized the miiuy croaker DIGIRR (mmi-DIGIRR) gene. The results of gene structure analysis indicated that there were differences between the mmi-DIGIRR and mammalian SIGIRR, which there were two immunoglobulin (Ig) domains contained in extracellular region of mmi-DIGIRR. Sequence alignment analysis showed that fish DIGIRR shared some conserved sequences with other vertebrates and the evolution was relatively conservative. In order to further validate the function of mmi-DIGIRR and its expression levels in various tissues of fish, qRT-PCR has been conducted. The results showed DIGIRR has significant expression levels in liver, skin and muscle while expression levels in heart are low. The LPS-induced NF-κB activation was inhibited by overexpression of DIGIRR significantly. In conclusion, the evolution and function of mmi-DIGIRR were comprehensively analyzed in this study, which would provide a theoretical basis for the future research of fish DIGIRR.

IRF3 enhances NF-κB activation by targeting IκBα for degradation in teleost fish

Tightly regulation of NF-κB signaling is essential to innate and adaptive immune responses, but its regulatory mechanism remains unclear in various organisms, especially teleost fish. In this study, we reported that IRF3 attenuates the inhibitory effect of IκBα on NF-κB activation in teleost fish. Overexpression of IRF3 can promote IκBα degradation, whereas its knockdown can relieve degradation of IκBα. IRF3 promoted the degradation of IκBα protein, but this effect could be inhibited by MG132 treatment. IRF3 is crucial for the polyubiquitination and proteasomal degradation of IκBα. Our findings indicate that IRF3 regulates NF-κB pathway by targeting IκBα for ubiquitination and degradation. This study provides novel evidence on the regulation of innate immune signaling pathways in teleost fish and thus provides new insights into the regulatory mechanisms in mammals.

microRNA-21 negatively regulates NF-κB signaling pathway via targeting IL1R1 in miiuy croaker

microRNAs (miR) are non-coding RNAs that regulates many biochemical processes, such as cell growth, proliferation and immune response. In this study, the regulation of microRNA-21 (miR-21) to the nuclear factor kappaB (NF-κB) signaling pathway by target IL1R1 has been researched in miiuy croaker. First, we predicted the target gene of miR-21 through bioinformatics, and found that IL1R1 is a direct target of miR-21. Then, we found that the over-expression of miR-21 mimics and the pre-miR-21 plasmid inhibits the luciferase levels of the wild-type of IL1R1-3'UTR. miR-21 inhibitors increase the luciferase levels of IL1R1-3'UTR. Additionally, we also observed that the miR-21 could negative regulate the IL1R1 at the level of translation. At last, this study will help to further understand the immunomodulatory mechanisms of miRNAs in teleost fish after being invaded by pathogens.

MicroRNA-155 promotes pro-inflammatory functions and augments apoptosis of monocytes/macrophages during Vibrio anguillarum infection in ayu, Plecoglossus altivelis

Upon recognition of pathogen-associated molecular patterns by pattern-recognition receptors, immune cells are recruited, and multiple antibacterial/viral signaling pathways are activated, leading to the production of immune-related cytokines, chemokines, and interferons along with further activation of the adaptive immune response. MicroRNAs (miRs) play essential roles in regulating such immune signaling pathways, as well as the biological activities of immune cells; however, knowledge regarding the roles of miRs in the immune-related function of monocytes/macrophages (MO/MΦ) remains limited in teleosts. In the present study, we addressed the effects of miR-155 on Vibrio anguillarum-infected MO/MΦ. Our results showed that miR-155 augmented MO/MΦ expression of proinflammatory cytokines and attenuated the expression of anti-inflammatory cytokines. Additionally, the phagocytosis and bacteria-killing abilities of these cells were boosted by miR-155 administration, which also promoted M1-type polarization but inhibited M2-type polarization. Furthermore, the V. anguillarum-infection-induced apoptosis was also enhanced by miR-155 mimic transfection, which might have been due to excessive inflammation or the accumulation of reactive oxygen species. These results represent the first report providing a detailed account of the regulatory roles of miR-155 on MO/MΦ functions in teleosts and offer insight into the evolutionary history of miR-155-mediated regulation of host immune responses.

Non-coding RNAs Function as Immune Regulators in Teleost Fish

Non-coding RNAs (ncRNAs) are functional RNA molecules that are transcribed from DNA but not translated into proteins. ncRNAs function as key regulators of gene expression and chromatin modification. Recently, the functional role of ncRNAs in teleost fish has been extensively studied. Teleost fish are a highly diverse group among the vertebrate lineage. Fish are also important in terms of aquatic ecosystem, food production and human life, being the source of animal proteins worldwide and models of biomedical research. However, teleost fish always suffer from the invasion of infectious pathogens including viruses and bacteria, which has resulted in a tremendous economic loss to the fishing industry worldwide. Emerging evidence suggests that ncRNAs, especially miRNAs and lncRNAs, may serve as important regulators in cytokine and chemokine signaling, antigen presentation, complement and coagulation cascades, and T cell response in teleost fish. In this review, we summarize current knowledge and understanding of the roles of both miRNAs and lncRNAs in immune regulation in teleost fish. Molecular mechanism insights into the function of ncRNAs in fish immune response may contribute to the development of potential biomarkers and therapeutic targets for the prevention and treatment of fish diseases.