Characterization of the black carp TRAF6 signaling molecule in innate immune defense

Involvement of tumor necrosis factor receptor-associated factor 6 (TRAF6) in NF-κB activation and antiviral immunity: Molecular and functional characterization of TRAF6 in red-spotted grouper (Epinephelus akaara)

Tumor necrosis factor receptor-associated factor 6 (TRAF6) is a member of the TRAF family of adaptor proteins involved in the signal transduction pathways of both TNF receptor and interleukin-1 receptor/Toll-like receptor superfamilies. In this study, red-spotted grouper (Epinephelus akaara) TRAF6 (EaTraf6) was identified and characterized. The open reading frame of EaTraf6, 1713 bp in length, encodes a putative protein of 570 amino acids and has a predicted molecular weight and theoretical isoelectric point of 64.11 kDa and 6.07, respectively. EaTraf6 protein contains an N-terminal RING-type zinc finger domain, two TRAF-type zinc finger domains, a coiled-coil region (zf-TRAF), and a conserved C-terminal meprin and TRAF homology (MATH) domain. EaTraf6 shared the highest amino acid sequence identity with its ortholog from Epinephelus coioides, and phylogenetic analysis showed all fish TRAF6s clustered together and apart from other species. qRT-PCR results revealed that EaTraf6 was ubiquitously expressed in all examined tissues, with the highest level detected in the blood. In the immune challenge, EaTraf6 exhibited modulated mRNA expression levels in the blood and spleen. The subcellular localization analysis revealed that the EaTraf6 protein was predominantly present in the cytoplasm; however, it could translocate into the nucleus following poly (I:C) stimulation. The antiviral function of EaTraf6 was confirmed by analyzing the expression of host antiviral genes and viral genomic RNA during viral hemorrhagic septicemia virus infection. Additionally, luciferase reporter assay results indicated that EaTraf6 is involved in the activation of the NF-κB signaling pathway upon poly (I:C) stimulation. Finally, the effect of EaTraf6 on cytokine gene expression and its role in regulating macrophage M1 polarization were demonstrated. Collectively, these findings suggest that EaTraf6 is a crucial immune-related gene that significantly contributes to antiviral functions and regulation of NF-κB activity in the red-spotted grouper.

Role of TRAF6 from obscure puffer (Takifugu obscurus) in immune response against Edwardsiella tarda infection

Tumor necrosis factor receptor-associated factor 6 (TRAF6) is a vital molecule of inflammatory signaling pathways in innate immune response against pathogens. To elucidate its role in defense against Edwardsiella tarda infection in teleost fish, TRAF6 homologue was identified from obscure puffer (Takifugu obscurus) and functionally analyzed in this study. The obscure puffer TRAF6 (ToTRAF6) is a protein of 565 amino acids containing conserved RING domain, zinc finger-TRAF and MATH_TRAF6 domain. ToTRAF6 mRNA distributed in various healthy tissues of obscure puffer and was upregulated in the immune related tissues after E. tarda infection. ToTRAF6 protein was localized in the cytoplasm and aggregate as dots around the nuclei in FHM cells. The overexpression of ToTRAF6 in FHM cells decreased the quantity of E. tarda and induced the significant upregulation of downstream MAPK signaling pathway genes. These data suggest that ToTRAF6 is a key molecule of MAPK signaling pathway in defense against E. tarda infection.

Characterization of TRAF genes and their responses to Vibrio anguillarum challenge in Argopecten scallops

The tumor necrosis factor receptor-related factor (TRAF) family has been reported to be involved in many immune pathways, such as TNFR, TLR, NLR, and RLR in animals. However, little is known about the roles of TRAF genes in the innate immune of Argopecten scallops. In this study, we first identified five TRAF genes, including TRAF₂, TRAF₃, TRAF₄, TRAF₆ and TRAF₇, but not TRAF₁ and TRAF₅, from both the bay scallop A. irradians (Air) and the Peruvian scallop A. purpuratus (Apu). The phylogenetic analysis showed that the TRAF genes in Argopecten scallops (AiTRAF) belong to the branch of molluscan TRAF family, which lacks TRAF₁ and TRAF₅. Since TRAF₆ is a key bridge factor in the tumor necrosis factor superfamily and plays an important role in innate and adaptive immunity, we cloned the ORFs of the TRAF₆ gene in both A. irradians and A. purpuratus, as well as in two reciprocal hybrids (Aip for the hybrid Air × Apu and Api for the hybrid Apu × Air). Differences in conformational and post-translational modification resulted from the variation in amino acid sequences may cause differences in activity among them. Analysis of conserved motifs and protein structural domains revealed that AiTRAF contains typical structural domains similar to those of other mollusks and has the same conserved motifs. Tissue expression of TRAF in Argopecten scallops challenged by Vibrio anguillarum was examined by qRT-PCR. The results showed that AiTRAF were higher in gill and hepatopancreas. When challenged by Vibrio anguillarum, the expression of AiTRAF was significantly increased compared with the control group, indicating that AiTRAF may play an important role in the immunity of scallops. In addition, the expression of TRAF was higher in Api and Aip than in Air when challenged by Vibrio anguillarum, suggesting that TRAF may have contributed to the high resistance of Api and Aip to Vibrio anguillarum. The results of this study may provide new insights into the evolution and function of TRAF genes in bivalves and ultimately benefit scallop breeding.

Structure of fish TRAF4 and its implication in TRAF4-mediated immune cell and platelet signaling

Due to an increasing interest in immunity and signal transduction in teleost fish, important key signaling molecules associated with the immune response, including TRAF molecules, have been recently cloned and characterized. To better understand the role of TRAF4 in fish immune signaling and compare it with the human system, our study cloned the TRAF4 gene from the Antarctic yellowbelly rockcod Notothenia coriiceps (ncTRAF4) and purified the protein. Here, we report the first crystal structure of teleost fish TRAF4. Based on biochemical characterization, our findings elucidated the mechanisms through which signaling molecules gain cold adaptivity. Additionally, we identified a platelet receptor GPIbβ homolog in N. coriiceps (ncGPIbβ) and found that the "RRFERLFKEARRTS" region of this homolog directly binds to ncTRAF4, indicating that ncTRAF4 also recognizes the "RLXA" motif for receptor interactions and further TARF4-mediated cellular signaling. Collectively, our findings provide novel insights into the mechanisms of TRAF4-mediated immune cell and platelet signaling in fish and the structural flexibility-mediated cold adaptiveness of signaling molecules.

Molecular characterization and expression analysis of TRIF, TRAF6, and TBK1 of golden pompano (Trachinotus ovatus)

Toll/IL-1R domain-containing adaptor-inducing IFN-β (TRIF), tumor necrosis factor receptor-associated factor 6 (TRAF6) and TANK-binding kinase 1 (TBK1) are critical signal transducers in toll-like receptors (TLRs) signaling pathway. In the present study, TRIF, TRAF6 and TBK1 were characterized from golden pompano (Trachinotus ovatus), named as TroTRIF, TroTRAF6 and TroTBK1, respectively. The full cDNA length of TroTRIF, TroTRAF6 and TroTBK1 was 2297 bp, 2293 bp, and 2482 bp, which respectively encoded 589, 573 and 723 amino acids. The deduced amino acids sequences of TroTRIF, TroTRAF6 and TroTBK1 contained conserved motifs, similar to their counterparts in other vertebrates. Phylogenetic tree analysis revealed that TroTRIF, TroTRAF6 and TroTBK1 were well clustered with their counterparts in other fish species. Quantitative Real-Time PCR (qPCR) analysis showed that TroTRIF, TroTBK1 and TroTRAF6 were detected in all examined tissues of healthy fish, but shared distinct transcript levels. Moreover, the expressions of TroTRIF, TroTBK1 and TroTRAF6 were generally induced by polyriboinosinic-polyribocytidylic acid (polyI:C), lipopolysaccharide (LPS), and Vibrio alginolyticus stimulation in vivo, indicating their critical roles in the immune defense of golden pompano against pathogen invasion. Our results provide valuable information for understanding the functions of these genes in golden pompano.

Black carp TUFM collaborates with NLRX1 to inhibit MAVS-mediated antiviral signaling pathway

TUFM is a mitochondrial protein and serves as a regulator of antiviral signaling; nevertheless, the character of TUFM in teleosts remains unidentified. In this study, TUFM homologue of black carp (Mylopharyngodon piceus) has been characterized and its role in innate immunity has been explored. Black carp TUFM (bcTUFM) comprises 447 amino acids and shows the high similarity to human TUFM. bcTUFM was about 50 kDa in the Western blot assay and was determined as a cytosolic protein by immunofluorescent microscopy. Knockdown of bcTUFM by shRNA enhanced the antiviral ability of the host cells. The induction fold of interferon promoter transcription in the cells co-expressing bcTUFM and bcMAVS was much lower than that of the cells expressing bcMAVS alone. Our previous study has identified that bcNLRX1 interacted with bcMAVS and functioned as an inhibitor of bcMAVS. The interaction between bcTUFM and bcNLRX1, but not bcTUFM and bcMAVS, was detected through co-immunoprecipitation. The subsequent reporter assay and plaque assay demonstrated that the inhibition of bcMAVS-mediated interferon production and antiviral activity by bcNLRX1 was enhanced by co-expressed bcTUFM. Thus, our data suggests that bcTUFM cooperates with bcNLRX1 to inhibit bcMAVS-mediated antiviral signaling during host antiviral innate immune response against SVCV.

TRIF-mediated antiviral signaling is differentially regulated by TRAF2 and TRAF6 in black carp

TRIF is an antiviral adaptor downstream of Toll-like receptors, the roles of teleost TRIF and their regulation remain largely unknown. In this study, a TRIF homologue (bcTRIF) of black carp (Mylopharyngodon piceus) has been cloned, and the transcription of bcTRIF in vivo and ex vivo increased in response to different stimuli. Overexpressed bcTRIF induced the transcription of interferon promoter in the EPC cells and enhanced protection of cells against infection of spring viremia of carp virus (SVCV). The previous study has identified that black carp TRAF2 (bcTRAF2) and TRAF6 (bcTRAF6) functioned positively in RIG-I/MAVS signaling. When co-expressed with bcTRAF2, bcTRIF-induced the transcription of interferon promoter in EPC cells was decreased, and the antiviral activity of bcTRIF was dampened accordingly. On the contrary, co-expressed bcTRAF6 enhanced both bcTRIF-mediated interferon promoter transcription and antiviral activity. The subsequent co-immunoprecipitation identified the interaction between bcTRAF2/6 and bcTRIF. Thus, bcTRIF-mediated antiviral signaling is up-regulated by bcTRAF6 and down-regulated by bcTRAF2.

Roles of TRAFs in Ischemia-Reperfusion Injury

Tumor necrosis factor receptor-associated factor (TRAF) proteins are a family of signaling molecules that function downstream of multiple receptor signaling pathways, and they play a pivotal role in the regulation of intracellular biological progresses. These TRAF-dependent signaling pathways and physiological functions have been involved in the occurrence and progression of ischemia-reperfusion injury (IRI), which is a common pathophysiological process that occurs in a wide variety of clinical events, including ischemic shock, organ transplantation, and thrombolytic therapy, resulting in a poor prognosis and high mortality. IRI occurs in multiple organs, including liver, kidney, heart, lung, brain, intestine, and retina. In recent years, mounting compelling evidence has confirmed that the genetic alterations of TRAFs can cause subversive phenotype changes during IRI of those organs. In this review, based on current knowledge, we summarized and analyzed the regulatory effect of TRAFs on the IRI of various organs, providing clear direction and a firm theoretical basis for the development of treatment strategies to manipulate TRAF proteins or TRAF-dependent signaling pathways in IRI-related diseases.

TLR13, TLR22, TRAF6, and TAK1 in the soiny mullet (Liza haematocheila): Molecular characterization and expression profiling analysis

Toll-like receptors (TLRs) and their associated signaling pathways play pivotal roles in the immune response to invading pathogens. Here, TLR13, TLR22, tumor necrosis factor receptor-associated factor 6 (TRAF6), and transforming growth factor-β-activated kinase1 (TAK1) were characterized in the soiny mullet (Liza haematocheila), representative mugilid species that is widely cultured in Asia. The four mullet genes, which shared characteristic features with their counterparts in other teleosts, were ubiquitously expressed in all of the examined tissues, albeit with different expression patterns. Following Streptococcus dysgalactiae infection, the four genes were upregulated to different degrees in various mullet tissues. These results indicated that the four genes were involved in the mullet immune response to bacterial infection. To the best of our knowledge, this is the first characterization of these four genes in mullet. Our results provide a basis for future studies of TLR signaling pathways in mullet, as well as for similar studies in other mugilids.

Black carp RIPK1 negatively regulates MAVS-mediated antiviral signaling during the innate immune activation

Receptor-interacting serine/threonine protein kinase 1 (RIPK1) is an important regulator of necroptosis and involved in innate immune response in human and mammal; however, its function in teleost fish mains largely unknown. In this paper, the RIPK1 homologue of black carp (Mylopharyngodon piceus) has been cloned and characterized to explore its role in immunity. Black carp RIPK1 (bcRIPK1) possesses the similar structure to its mammalian counterpart, which has been identified as a cytosolic protein by immunofluorescence staining. Overexpressed bcRIPK1 in host cells led to the decreased transcription of interferon (IFN) and interferon stimulated genes, and exogenous bcRIPK1 in EPC cells led to the decreased transcription of interferon promoters in reporter assay. Our previous study has identified that black carp MAVS (bcMAVS) functions as an antiviral adaptor protein against both grass carp reovirus (GCRV) and spring viremia of carp virus (SVCV). The reporter assay showed that the IFN-inducing ability of bcMAVS was dampened by bcRIPK1 and the plaque assay demonstrated that the antiviral activity of bcMAVS was inhibited by bcRIPK1. The immunofluorescent staining and co-immunoprecipitation identified the interaction between these two molecules. Thus, the data generated in this paper support the conclusion that bcRIPK1 interacts with bcMAVS and negatively regulates bcMAVS-mediated antiviral signaling.

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.

Fish TRAF2 promotes innate immune response to RGNNV infection

Tumour necrosis factor receptor-associated factors (TRAFs) are key regulatory proteins in the NF-κB signaling pathways. TRAF2 participates in the activation of both canonical and non-canonical NF-κB pathways, which are crucial for cell inflammation and cell survival. To elucidate its function in teleost fish, TRAF2 homologues of yellow grouper (Epinephelus awoara) and golden pompano (Trachinotus ovatus) have been cloned and characterized in this study. The open reading frame (ORF) of grouper TRAF2 (EaTRAF2) consists of 1563 nucleotides encoding a 521 amino acid protein with a predicted molecular mass of 58.70 kDa. The ORF of golden pompano TRAF2 (ToTRAF2) consists of 1563 nucleotides encoding a 521 amino acid protein with a predicted molecular mass of 58.66 kDa EaTRAF2 and ToTRAF2 share 99.23% and 99.42% identity with orange-spotted grouper (Epinephelus coioides) TRAF2 (EcTRAF2), respectively. Quantitative real-time PCR analysis indicated that the expression of EaTRAF2 was increased in grouper spleen (GS) cells after Red-spotted grouper nervous necrosis virus (RGNNV) infection; while the expression of ToTRAF2 was decreased in golden pompano brain (TOGB) cells after RGNNV infection. Both EaTRAF2 and ToTRAF2 were identified as a cytosolic protein and suggested to be associated with vesicles scattering in the cytoplasm. Both EaTRAF2 and ToTRAF2 enhanced RGNNV replication during viral infection in vitro. Further studies showed that EaTRAF2 and ToTRAF2 overexpression decreased the expression levels of interferon associated cytokines and pro-inflammatory factors. Taken together, these results are important for better understanding of the function of TRAF2 in fish and reveal its involvement in host response to immune challenges in RGNNV.

Genome-wide characterization of TNF receptor-associated factors in the Chinese soft-shelled turtle Pelodiscus sinensis and their expression profiling in response to Aeromonas hydrophila challenge

Tumor necrosis factor receptor (TNFR)-associated factors (TRAFs) are a family of crucial signaling molecules that mediate the signal transduction of various immune signaling pathways. Extensive studies have demonstrated that TRAFs play vital roles in regulating cellular immune responses. However, the biological functions and expression profiling of TRAFs in Chinese soft-shelled turtle (Pelodiscus sinensis) remain unclear. In this study, the genes of the PsTRAF family at the genome-wide level were identified in P. sinensis, revealing six PsTRAF members that contained the conserved TRAF domain in the C-terminal regions. Molecular evolutionary analysis showed that PsTRAFs shared close evolutionary relationships and similar protein crystal structures with the TRAF homologs from other turtles, indicating the evolutionary conservation of PsTRAFs. Further expression analysis revealed the tissue-specific expression of PsTRAF genes. Obvious variations in the expression of PsTRAF genes were observed in the spleen in response to Aeromonas hydrophila infection. Three PsTRAF genes, PsTRAF2, PsTRAF3, and PsTRAF6, were significantly upregulated at the mRNA and protein levels post-infection, indicating their potential function in the immune response. Moreover, the protein-protein associations of PsTRAFs with several signaling receptors were predicted in P. sinensis. These results provide a basis for the investigation of the functional roles of PsTRAFs in immune defense against bacterial infection.

Comprehensive Evolutionary Analysis of Lamprey TNFR-Associated Factors (TRAFs) and Receptor-Interacting Protein Kinase (RIPKs) and Insights Into the Functional Characterization of TRAF3/6 and RIPK1

TNFR-associated factors (TRAFs) and receptor-interacting protein kinases (RIPKs) are important immunological linker molecules in mammals and play important roles in the TNFα, TLR and IFN signaling pathways. However, the evolutionary origins of these genes in vertebrates have not previously been described in lampreys. In this study, we searched the genomes of Lampetra japonicum, Lethenteron reissneri, and Petromyzon marinus for genes encoding trafs and ripks and performed homologous sequence alignment, phylogenetic tree, functional domain, conserved motif, gene structure, and synteny analyses to determine their evolutionary relationships. The distribution of the lamprey traf and ripk families and the immune response of the gene families in lampreys stimulated by different pathogens were also demonstrated, suggesting a role of structural changes in expression and functional diversification. Additionally, the dual luciferase reporter gene assay showed that the addition of exogenous immunomodulator (TNFα or IFN) to the overexpression of LjLRIPK1a or LjTRAF3/6 significantly downregulated NF-κB or ISRE activation. LjRIPK1a can significantly enhance caspase-8 activity, and overexpression of LjRIPK1a or LjTRAF3a/6 in HEK293T cells results in cell apoptosis. In summary, this study makes an important contribution to the understanding of the traf and ripk gene families in different vertebrates. Our results also provide new evidence for the evolution of vertebrate TRAFs and RIPKs and their impacts on immune regulation.

Identification and characterization of IRF9 from black carp Mylopharyngodon piceus

Interferon regulatory factor 9 (IRF9) plays a crucial role in JAK-STAT signaling in human and mammal. However, the relationship between IRF9 and STAT1 in teleost fish remains largely unknown. The previous study has elucidated that two STAT1 isoforms (bcSTAT1a and bcSTAT1b) of black carp (Mylopharyngodon piceus) play an important role during the innate immune activation initiated by grass carp reovirus (GCRV). In this paper, black carp IRF9 (bcIRF9) has been identified and characterized. bcIRF9 was distributed majorly in the nucleus and the linker domain (LD) of bcIRF9 was vital for its nuclear localization. bcIRF9 showed ISRE-inducing activity in reporter assay and presented antiviral activity against GCRV in plaque assay, in which both DNA binding domain (DBD) and LD of bcIRF9 were essential for its antiviral signaling. bcIRF9 was identified to interact with both bcSTAT1a and bcSTAT1b in the co-immunoprecipitation assay. It was interesting that bcIRF9-mediated antiviral signaling was up-regulated by bcSTAT1a; however, down-regulated by bcSTAT1b. Thus, our data support the conclusion that bcIRF9 plays an important role in the innate immune defense against GCRV, in which two STAT1 proteins function differently.

Genome-wide identification, characterization, and expression analysis of the TRAF gene family in Chinese tongue sole (Cynoglossus semilaevis)

Tumor necrosis factor (TNF) receptor-associated factors (TRAFs) play crucial roles as signaling mediators for the TNF receptor (TNFR) superfamily and the interleukin-1 receptor/Toll-like receptor (IL-1R/TLR) superfamily. TRAFs collectively play important roles in multiple biological processes and organismal immunity. However, systematic identification of the TRAF gene family in teleost fish has not yet been reported, and there is little available information about its roles in innate immunity in Chinese tongue sole (Cynoglossus semilaevis), an aquaculture fish of high economic value. In the present study, we identified and characterized seven TRAF genes, namely, CsTRAF2a, CsTRAF2b, CsTRAF3, CsTRAF4, CsTRAF5, CsTRAF6 and CsTRAF7, in Chinese tongue sole, and the complete ORFs of the CsTRAFs were cloned. Sequence analysis revealed various genomic structures of the CsTRAFs and showed that they contain typical conserved domains compared with mammalian TRAFs. Phylogenetic analysis indicated the evolutionary relationships of TRAF family members in teleost fish and revealed an absence of TRAF1 in most species and TRAF5 in some species of teleosts. Analysis of the gene structures and motifs showed the diversity and distribution of exon-intron structures and conserved motifs in Chinese tongue sole and several other teleost species. Real-time quantitative PCR was used to investigate the expression patterns of CsTRAF genes in tissues of healthy fish and in the gills, livers and spleens of fish after bacterial infection with Vibrio harveyi. The results indicate that only CsTRAF2a is relatively highly expressed in the brain and that the other CsTRAFs are highly expressed in immune-related tissues and may participate in the immune response after infection with pathogenic bacteria. Functional analysis of CsTRAF3, CsTRAF4 and CsTRAF6 revealed that only CsTRAF6 could strongly activate the NF-кB pathway after overexpression of CsTRAF3, CsTRAF4 and CsTRAF6 in HEK-293T cells. This systematic analysis provided valuable information about the diverse roles of TRAFs in the innate immune response to pathogenic bacterial infection in teleost fish and will contribute to the functional characterization of CsTRAF genes in further research.

Expression and functional analysis of tumor necrosis factor receptor (TNFR)-associated factor 5 from Nile tilapia, Oreochromis niloticus

Nile tilapia (Oreochromis niloticus) is a pivotal economic fish that has been plagued by Streptococcus infections. Tumor necrosis factor receptor-associated factor 5 (TRAF5) is a crucial adaptor molecule, which can trigger downstream signaling cascades involved in immune pathway. In this study, Nile tilapia TRAF5 coding sequence (named OnTRAF5) was obtained, which contained typical functional domains, such as RING, zinc finger, coiled-coil and MATH domain. Different from other TRAF molecules, OnTRAF5 had shown relatively low identify with its homolog, and it was clustered into other teleost TRAF5 proteins. qRT-PCR was used to analysis the expression level of OnTRAF5 in gill, skin, muscle, head kidney, heart, intestine, thymus, liver, spleen and brain, In healthy Nile tilapia, the expression level of OnTRAF5 in intestine, gill and spleen were significantly higher than other tissues. While under Streptococcus agalactiae infection, the expression level of OnTRAF5 was improved significantly in all detected organs. Additionally, over-expression WT OnTRAF5 activated NF-κB, deletion of RING or zinc finger caused the activity impaired. In conclusion, OnTRAF5 participate in anti-bacteria immune response and is crucial for the signaling transduction.

NLRX1 of black carp suppresses MAVS-mediated antiviral signaling through its NACHT domain

NOD-like receptor (NLR) family member X1 (NLRX1) of human localizes on mitochondria and serves as a negative regulator of antiviral signaling. However, the function of NLRX1 in teleost fish still remains elusive. To explore its role in the innate immunity of teleost fish, NLRX1 homologue has been cloned and characterized from black carp (Mylopharyngodon piceus). Black carp NLRX1 (bcNLRX1) consists of 1008 amino acids, which includes a N-terminal mitochondrial targeting sequence, a central NACHT domain and a C-terminal leucine-rich repeat (LRR) domain. bcNLRX1 was identified as a cytosolic protein locating on mitochondria through immunofluorescence (IF) staining. The overlapped subcellular distribution of bcNLRX1 and black carp MAVS (bcMAVS) was detected in IF staining, and the direct interaction between these two molecules in vitro was identified through co-immunoprecipitation assay. When co-expressed with bcMAVS, bcNLRX1 fiercely reduced bcMAVS-mediated IFN induction in reporter assay. Accordingly, the antiviral activity of bcMAVS against both grass carp reovirus (GCRV) and spring viremia of carp virus (SVCV) was forcefully repressed by bcNLRX1 in plaque assay. Mutagenic analyses further revealed that the NACHT domain of bcNLRX1 was essential for it to interact with bcMAVS and to suppress bcMAVS-mediated antiviral signaling. Taken together, our data support the conclusion that bcNLRX1 negatively regulates bcMAVS-mediated antiviral signaling through its NACHT domain during host innate immune activation.

Molecular cloning and expression analysis of MyD88 and TRAF6 in Qihe crucian carp Carassius auratus

Myeloid differentiation factor 88 (MyD88) and tumor necrosis factor receptor-associated factor 6 (TRAF6) are two critical signal transducers in toll-like receptor (TLR) pathway. In the present study, we identified and characterized the homologues of MyD88 and TRAF6 in Qihe crucian carp Carassius auratus, termed as CaMyD88 and CaTRAF6, respectively, and examined their roles during pathogenic infection. Full-length cDNA of CaMyD88 was 2463 bp, including a 191 bp 5'-untranslated region (UTR), a 1417 bp 3'-UTR, and an 855 bp open reading frame (ORF) encoding for a putative protein with 284 amino acids. Full-length cDNA of CaTRAF6 was identified to be 2555 bp, consisting of a 52 bp 5'-UTR, an 871 bp 3'-UTR, and a 1632 bp ORF encoding a protein of 543 amino acids. Deduced amino acid sequences of CaMyD88 and CaTRAF6 contained the typical domains (CaMyD88: death domain and TIR domain; CaTRAF6: one RING-type zinc finger domain, two TRAF-type zinc finger domains, one coiled-coil region, and one conserved C-terminal meprin and TRAF homology domain) as in other fish. Quantitative Real-Time PCR (qRT-PCR) analysis revealed that both CaMyD88 and CaTRAF6 were ubiquitously expressed throughout the development stages and appeared to be developmentally regulated. In addition, CaMyD88 and CaTRAF6 had a broadly distribution of expression in all examined eleven tissues of healthy fish, although the transcript levels varied among the different tissues. Moreover, it was found that mRNA expressions of CaMyD88 and CaTRAF6 were generally up-regulated after stimulation by polyI:C, flagellin, and Aeromonas hydrophila in spite of the down-regulation appeared at some time points or tissues. These results indicated that CaMyD88 and CaTRAF6 play the critical roles in the immune defense of Qihe crucian carp against pathogenic invasion. The present findings will provide the valuable information for understanding the innate immune responses of Qihe crucian carp and contribute to develop the preventive way against pathogens.

Molecular characteristics and function study of TNF receptor-associated factor 5 from grouper (Epinephelus coioides)

Tumor necrosis factor receptor-associated factor 5 (TRAF5) is a key adapter molecule that participates in numerous signaling pathways. The function of TRAF5 in fish is largely unknown. In the present study, a TRAF5 cDNA sequence (EcTRAF5) was identified in grouper (Epinephelus coioides). Similar to its mammalian counterpart, EcTRAF5 contained an N-terminal RING finger domain, a zinc finger domain, a C-terminal TRAF domain, including a coiled-coil domain and a MATH domain. The EcTRAF5 protein shared relatively low sequence identity with that of other species, but clustered with TRAF5 sequences from other fish. Real-time PCR analysis revealed that EcTRAF5 mRNA was broadly expressed in numerous tissues, with relatively high expression in skin, hindgut, and head kidney. Additionally, the expression of EcTRAF5 was up-regulated in gills and head kidney after infection with Cryptocaryon irritans. Intracellular localization analysis demonstrated that the full-length EcTRAF5 protein was uniformly distributed in the cytoplasm; while a deletion mutant of the coiled-coil domain of EcTRAF5 was observed uniformly distributed in the cytoplasm and the nucleus. After exogenous expression in HEK293T cells, TRAF5 significantly activated NF-κB. The deletion of the EcTRAF5 RING domain or of the zinc finger domain dramatically impaired its ability to activate NF-κB, implying that the RING domain and the zinc finger domain are required for EcTRAF5 signaling.

Molecular cloning and functional characterization of TRAF6 and TAK1 in rainbow trout, Oncorhynchus mykiss

TRAF6 and TAK1 are known to play important roles in vertebrate innate immunity as molecular bridge, linking upstream toll-like receptors (TLRs) with the downstream MAPK and NF-κB signalling pathways. However, their roles in TLR signalling pathway have yet to be fully described in fish. Here we identified genes encoding TRAF6 (OmTRAF6) and TAK1 (OmTAK1) from rainbow trout, Oncorhynchus mykiss, and examined their roles during pathogenic infections. The deduced amino acid sequences of OmTRAF6 and OmTAK1 contained the characteristic domains conserved in the TRAF and TAK1 families, respectively (OmTRAF6: RING, two TRAF-type zinc fingers, CCR and MATH domains; OmTAK1: STKc and CCR domains). In RTH-149 cells, the expression of OmTRAF6 and OmTAK1 was increased by stimulation with Edwardsiella tarda and LPS. Silencing of OmTRAF6 and OmTAK1 in RTH-149 cells negatively regulated the LPS-induced phosphorylation of p38 MAPK and JNK. TAK1 inhibitor (5z)-7-Oxozeaenol significantly decreased the LPS-induced activation of NF-κB in RTH-149 cells. In addition, silencing of OmTRAF6 and OmTAK1 significantly decreased the expression of MAPKs and NF-κB downstream target genes induced by LPS in RTH-149 cells. These findings suggest that OmTRAF6 and OmTAK1 might function like those of mammals to regulate bacteria-triggered signalling pathway in fish.

SIKE of black carp is a substrate of TBK1 and suppresses TBK1-mediated antiviral signaling

RIG-I like receptor (RLR) signaling functions importantly in host innate immune response against RNA virus, which is tightly regulated by a number of mechanisms to prevent aberrant interferon production. The suppressor of IKKε (SIKE) has been identified as a suppressor of IKKε and TBK1, which are key components of RLR signaling. In this study, SIKE homologue (bcSIKE) of black carp (Mylopharyngodon piceus) has been cloned and characterized. The transcription of bcSIKE varied in host cells in response to the stimulation of LPS, poly (I:C) and viruses. bcSIKE migrated around 27 KDa in immunoblot assay and distributed in both cytoplasm and nucleus of host cell in immunofluorescent (IF) staining test. bcSIKE showed no IFN-inducing ability in reporter assay and EPC cells expressing bcSIKE showed no enhanced antiviral ability against either grass carp reovirus (GCRV) or spring viremia of carp virus (SVCV). However, bcSIKE obviously dampened the IFN-inducing ability of RLR signaling members in reporter assay when bcSIKE was co-expressed with these molecules in EPC cells. The association between bcSIKE and bcTBK1 has been identified through IF and co-immunoprecipitation (co-IP) assay. The plaque assay demonstrated clearly that bcTBK1-mediated antiviral activity in EPC cells against both GCRV and SVCV was down regulated by bcSIKE. All the data generated in this paper support the conclusion that bcSIKE interacts with bcTBK1 and inhibits bcTBK1-mediated antiviral signaling during host innate immune activation, which is reported in teleost for the first time.

TAK1 of black carp positively regulates IRF7-mediated antiviral signaling in innate immune activation

Transforming growth factor β-activated kinase 1 (TAK1) plays a vital role in IL-1-mediated NF-κB, JNK, and p38 activation in human and mammals. However, the function of TAK1 in teleost fish still remains largely unknown. To explore the role of TAK1 during the antiviral innate immune response of teleost fish, TAK1 of black carp (Mylopharyngodon piceus) was cloned and characterized in this paper. The open reading frame (ORF) of black carp TAK1 (bcTAK1) consists of 1626 nucleotides and the predicted bcTAK1 protein contains 541 amino acids, which includes a N-terminal Serine/Threonine protein kinases (S/TKc) and a C-terminal coiled-coil region. bcTAK1 migrated around 75 kDa in immunoblotting assay and was identified as a cytosolic protein by immunofluorescence staining. bcTAK1 transcription in Mylopharyngodon piceus kidney (MPK) cells varied in response to the stimulation of poly (I:C), LPS, grass carp reovirus (GCRV), and spring viremia of carp virus (SVCV). bcTAK1 showed deficient IFN-inducing ability in reporter assay and feeble antiviral activity against GCRV and SVCV in plaque assay. However, when co-expressed with bcIRF7 in EPC cells, bcTAK1 obviously enhanced bcIRF7-mediated IFN promoter induction in reporter assay. Accordingly, the data of plaque assay demonstrated that the antiviral activity of bcIRF7 against both GCRV and SVCV was unregulated by bcTAK1. Thus, the data generated in this study support the conclusion that bcTAK1 up-regulates bcIRF7-mediated antiviral signaling during host innate immune activation, which is reported for the first time in vertebrates.

TRAF3 enhances STING-mediated antiviral signaling during the innate immune activation of black carp

Tumor necrosis factor receptor-associated factor 3 (TRAF3) is a main regulator of antiviral and anti-inflammatory pathways in mammals, which is considered to induce type I interferon (IFN) activation and negatively regulate the activation of the canonical and non-canonical NF-κB pathways. To elucidate its function in teleost fish, TRAF3 homologue of black carp (Mylopharyngodon piceus) has been cloned and characterized in this study. The open reading frame (ORF) of black carp TRAF3 (bcTRAF3) consists of 1722 nucleotides and bcTRAF3 contains 574 amino acids. bcTRAF3 protein migrated around 65 KDa in immunoblot analysis of both EPC and HEK293T cells. bcTRAF3 was identified as a cytosolic protein and suggested to form aggregates or be associated with vesicles scattering in the cytoplasm. It was interesting that both NF-κB and IFN transcription was activated by bcTRAF3 in reporter assay. When co-expressed with black carp STING (bcSTING), bcTRAF3 was redistributed in the cytoplasm and its subcellular location overlapped with that of bcSTING no matter what the cells was infected with GCRV or not, which suggested the association between these two molecules. bcSTING-mediated IFN production was up-regulated by bcTRAF3 in a dose dependent manner in reporter assay. Accordingly, EPC cells transfected with both bcSTING and bcTRAF3 showed enhanced antiviral activity comparing EPC cells expressing bcSTING alone. Taken together, the data generated in this paper supported the conclusion that bcTRAF3 was recruited into host innate immune activation and positively regulated bcSTING-mediated antiviral signaling.

Molecular cloning and characterization of TANK of black carp Mylopharyngodon piceus

The TRAF family member-associated NF-κB activator (TANK) is linked to the regulation of the transcription of NF-κB in mammals; however, its role in interferon induction is unclear. To elucidate the roles of TANK in teleost, the TANK homologue of black carp (Mylopharyngodon piceus) has been cloned and characterized in this paper. The open reading frame (ORF) of black carp TANK (bcTANK) comprises 1050 nucleotides and the predicted bcTANK protein contains 350 amino acids. The transcription of bcTANK in host cells increased in response to the stimulation of LPS, poly (I:C), SVCV and GCRV. bcTANK migrated around 50 KDa in immunoblot assay and was identified as a cytosolic protein by immunofluorescent staining in both EPC and HeLa cells. bcTANK could not induce the activity of IFN promoter in luciferase reporter assay in EPC cells; however, the IFN-activation ability of bcTANK was obviously enhanced when the cells were treated with LPS, poly (I:C) or virus. Both CPE ratio and virus titer in the media of EPC cells expressing bcTANK were obviously lower than those of the control cells, which were examined by violet crystal staining and plaque assay separately. Taken together, our data support the conclusion that bcTANK plays an important role in the antiviral innate immune activation of black carp.

Identification of tumor necrosis factor receptor-associated factor 6 in the pearl mussel Hyriopsis cumingii and its involvement in innate immunity and pearl sac formation

Tumor necrosis factor receptor-associated factor 6 (TRAF6) acts as a central intracellular signal adapter molecule that mediates the tumor necrosis factor receptor superfamily and the interleukin-1 receptor/Toll-like receptor family in vertebrates and invertebrates. In the present study, HcTRAF6, a molluscan homologue of TRAF6 from Hyriopsis cumingii, has been cloned and identified. The entire open reading frame of HcTRAF6 was found to comprise a 1965-bp region that encodes a predicted protein of 654 amino acids, which contains conserved characteristic domains including a RING domain, two TRAF-type zinc finger domains, a typical coiled coil and the MATH domain. Phylogenetic analysis revealed that HcTRAF6 was aggregated closely with CsTRAF6 from Cyclina sinensis in the invertebrate cluster of mollusks. Further, qRT-PCR analysis showed that HcTRAF6 mRNA was extensively distributed in mussel tissues with a high expression in gills. After immune stimulation with Aeromonas hydrophila and lipopolysaccharides, the transcription of HcTRAF6 was obviously induced in the gills and hemocytes. In addition, significant fluctuation in HcTRAF6 expression was observed in the pearl sac, gills and hemocytes after mantle implantation. These findings confirmed its role in the alloimmune response. Dual-luciferase reporter assay showed that over-expression of HcTRAF6 could enhance the activity of the NF-κB reporter in a dose-dependent manner. Further, the RNA interference showed that the up-regulation of antimicrobial peptides in anti-bacterial infection was strongly suppressed in HcTRAF6-silenced mussels and that depletion of HcTRAF inhibited the elimination of A. hydrophila. All these findings together prove that HcTRAF6 functions as an efficient regulator in innate immune mechanisms against invading pathogens and the alloimmune mechanism after mantle implantation in H. cumingii.

Molecular cloning and functional analysis of tumor necrosis factor receptor-associated factor 6 (TRAF6) in thick shell mussel, Mytilus coruscus

Tumor necrosis factor receptor-associated factor 6 (TRAF6) is one of the key adapter molecules in Toll-like receptor signal transduction that triggers downstream cascades involved in innate immunity. Despite of the well study in vertebrates, there is few data ascribe to this TRAF member in invertebrates, especially in bivalves. In the present study, a novel TRAF6 homologue termed McTRAF6 was firstly characterized in Mytilus coruscus. Like its counterparts in mammals, McTRAF6 shared the domain topology containing one RING domain, two zinc finger domains, one coiled-coil region and a MATH domain. McTRAF6 transcripts predominantly expressed in gills, digestive glands and hemocytes in M. coruscus, and were significantly up-regulated in hemocytes after challenge with lipopolysaccharide (LPS) and polyinosine-polycytidylic acid (poly I:C). Further, the subcellular localization in cytoplasm and the activation of Nk-κB or ISRE luciferase reporter by overexpressed McTRAF6 were identified in HEK293T cells. These results collectively indicate that McTRAF6 is a member of TRAF6 subfamily and plays a potential role in immune defense system against pathogenic agents invasions in thick shell mussel. To our knowledge, this is the first report on component of TLR signaling pathway in thick shell mussel, providing further evidence for the existence of TLR pathway in M. coruscus and contribute to clarify the innate immune system of thick shell mussel.

TRAF2 of black carp upregulates MAVS-mediated antiviral signaling during innate immune response

Tumor necrosis factor receptor-associated factor 2 (TRAF2) is a crucial component of the tumor necrosis factor (TNF) mediated signaling of higher vertebrates. To elucidate its function in teleost fish, TRAF2 homologue of black carp (Mylopharyngodon piceus) has been cloned and characterized in this study. The open reading frame (ORF) of black carp TRAF2 (bcTRAF2) consists of 1611 nucleotides and bcTRAF2 contains 536 amino acids. bcTRAF2 protein migrated around 65 KDa in immunoblot analysis of both EPC and HEK293T cells. bcTRAF2 was identified as a cytosolic protein and suggested to be associated with vesicles scattering in the cytoplasm. NF-κB transcription instead of IFN transcription was activated by bcTRAF2 in reporter assay. It was interesting that bcMAVS-mediated IFN production was up-regulated by bcTRAF2 in a dose dependent manner in reporter assay. Accordingly, EPC cells transfected with both bcMAVS and bcTRAF2 showed enhanced antiviral activity comparing EPC cells only expressing bcMAVS. When co-expressed with bcMAVS, bcTRAF2 was redistributed in the cytoplasm and its subcellular location overlapped with the subcellular location of bcMAVS, which suggested the association between these two molecules. Taken together, the data generated in this paper supported the conclusion that bcTRAF2 was recruited into host innate immune response and positively regulated bcMAVS-mediated antiviral signaling.

TBK1 of black carp plays an important role in host innate immune response against SVCV and GCRV

Tank-binding kinase 1 (TBK1) plays a pivotal role in the induction of type I IFNs in higher vertebrates. To explore the function of TBK1 in teleost, TBK1 of black carp (Mylopharyngodon Piceus) was cloned and characterized in this paper. The full-length cDNA of black carp TBK1 (bcTBK1) consists of 2857 nucleotides and the predicted bcTBK1 protein contains 727 amino acids, which includes an N-terminal kinase domain (KD), an ubiquitin-like domain (ULD) and two C-terminal coiled-coils. The transcription of bcTBK1 was constitutively detected in all the selected tissues and bcTBK1 mRNA level was increased in all selected tissues in response to SVCV or GCRV infection except that in muscle post GCRV invasion. The transcription of bcTBK1 in Mylopharyngodon Piceus fin (MPF) cells was up-regulated by the stimulation of SVCV, GCRV or poly (I:C) but not by LPS treatment. bcTBK1 migrated around 80 kDa in immunoblot assay and was identified as a cytosolic protein by immunofluorescence staining. bcTBK1 showed strong IFN-inducing ability in reporter assay and presented strong antiviral activity against both GCRV and SVCV in EPC cells. The reporter assay demonstrated that TRAF6 of black carp (bcTRAF6) up-regulated bcTBK1-induced IFN expression and the subcellular distribution of bcTBK1 overlapped with that of bcTRAF6 when these two proteins were co-expressed in EPC cells. Taken together, our study support the conclusion that bcTBK1 plays an important role in the antiviral innate immune response of black carp against SVCV and GCRV, in which its activity was positively regulated by bcTRAF6.