Anti-virus effects of interferon regulatory factors (IRFs) identified in ascidian Ciona savignyi

Interferon regulatory factors inhibit TiLV replication by activating interferon-a3 in tilapia (Oreochromis niloticus)

Tilapia lake virus (TiLV) is an emerging virus that seriously threatens the tilapia industries worldwide. Interferon regulatory factors (IRFs), which are the crucial mediators regulating the response of interferon (IFN) to combat invading viruses, have not yet been reported in tilapia during TiLV infection. Here, six IRF (IRF1, IRF2, IRF4, IRF7, IRF8, and IRF9) homologs from tilapia were characterized and analyzed. These IRFs typically shared the conserved domains and phylogenetic relationship with IRF homologs of other species. Tissue distribution analysis showed that all six IRF genes were expressed in various tissues, with the highest expression in immune-related tissues. Furthermore, overexpression of IRFs in tilapia brain (TiB) cells significantly inhibited TiLV propagation, as evidenced by decreased viral segment 8 gene transcripts and copy numbers of viral segment 1. More importantly, all six IRF genes significantly enhanced the promoter activity of type I interferon-a3 (IFNa3) in TiB cells, suggesting that tilapia IRF genes serve as positive regulators in activating IFNa3. Surprisingly, the promoter activity of IFNa3 mediated by IRF genes was markedly inhibited post-TiLV infection, indicating that TiLV antagonized IRF-mediated IFN immune response. Taken together, six IRF genes of tilapia are highly conserved transcription factors that inhibit TiLV infection by activating the promoter of IFNa3, which is in turn restrained by TiLV. These findings broaden our knowledge about the functionality of IRF-mediated antiviral immunity in tilapia against TiLV infection and host-TiLV interaction, which lays a foundation for developing antiviral strategies in tilapia cultural industries.

Correlative analysis of transcriptome and proteome in Penaeus vannamei reveals key signaling pathways are involved in IFN-like antiviral regulation mediated by interferon regulatory factor (PvIRF)

Interferon regulatory factors (IRFs) are crucial transcription factors that regulate interferon (IFN) induction in response to pathogen invasion. The regulatory mechanism of IRF has been well studied in vertebrates, but little has been known in arthropods. Therefore, in order to obtain new insights into the potential molecular mechanism of Peneaus vannamei IRF (PvIRF) in response to viral infection, comprehensive comparative analysis of the transcriptome and proteome profiles in shrimp infected with WSSV after knocking down PvIRF was conducted by using RNA sequencing (RNA-seq) and isobaric tags for relative and absolute quantification (iTRAQ). The sequence characterization, molecular functional evolution and 3D spatial structure of PvIRF were analyzed by using bioinformatics methods. PvIRF share the higher homology with different species in N-terminal end (containing DNA binding domain (DBD) including DNA sequence recognition sites and metal binding site) than that in C-terminal end. Within 4 IRF subfamilies of vertebrates, PvIRF had closer relationship with IRF1 subfamily. The DBD of PvIRF and C. gigas IRF1a were composed of α-helices and β-folds which was similar with the DBD structure of M. musculus IRF2. Interestingly, different from the five Tryptophan repeats highly homologous in the DBD of vertebrate IRF, the first and fifth tryptophans of PvIRF mutate to Phenylalanine and Leucine respectively, while the mutations were conserved among shrimp IRFs. RNAi knockdown of PvIRF gene by double-strand RNA could obviously promote the in vivo propagation of WSSV in shrimp and increase the mortality of WSSV-infected shrimp. It suggested that PvIRF was involved in inhibiting the replication of WSSV in shrimp. A total of 8787 transcripts and 2846 proteins were identified with significantly differential abundances in WSSV-infected shrimp after PvIRF knockdown, among which several immune-related members were identified and categorized into 10 groups according to their possible functions. Furthermore, the variation of expression profile from members of key signaling pathways involving JAK/STAT and Toll signaling pathway implied that they might participate IRF-mediated IFN-like regulation in shrimp. Correlative analyses indicated that 722 differentially expressed proteins (DEPs) shared the same expression profiles with their corresponding transcripts, including recognition-related proteins (CTLs and ITGs), chitin-binding proteins (peritrophin), and effectors (ALFs and SWD), while 401 DEPs with the opposite expression profiles across the two levels emphasized the critical role of post-transcriptional and post-translational modification. The results provide candidate signaling pathway including pivotal genes and proteins involved in the regulatory mechanism of interferon mediated by IRF on shrimp antiviral response. This is the first report in crustacean to explore the IFN-like antiviral regulation pathway mediated by IRF on the basis of transcriptome and proteomics correlative analysis, and will provide new ideas for further research on innate immune and defense mechanisms of crustacean.

Genome-Wide Identification, Comparison, and Expression Analysis of Transcription Factors in Ascidian Styela clava

Tunicates include diverse species, as they are model animals for evolutionary developmental biology study. The embryonic development of tunicates is known to be extensively regulated by transcription factors (TFs). Styela clava, the globally distributed invasive tunicate, exhibits a strong capacity for environmental adaptation. However, the TFs were not systematically identified and analyzed. In this study, we reported 553 TFs categorized into 60 families from S. clava, based on the whole genome data. Comparison of TFs analysis among the tunicate species revealed that the gene number in the zinc finger superfamily displayed the most significant discrepancy, indicating this family was under the highly evolutionary selection and might be related to species differentiation and environmental adaptation. The greatest number of TFs was discovered in the Cys2His2-type zinc finger protein (zf-C2H2) family in S. clava. From the point of temporal view, more than half the TFs were expressed at the early embryonic stage. The expression correlation analysis revealed the existence of a transition for TFs expression from early embryogenesis to the later larval development in S. clava. Eight Hox genes were identified to be located on one chromosome, exhibiting different arrangement and expression patterns, compared to Ciona robusta (C. intestinalis type A). In addition, a total of 23 forkhead box (fox) genes were identified in S. clava, and their expression profiles referred to their potential roles in neurodevelopment and sensory organ development. Our data, thus, provides crucial clues to the potential functions of TFs in development and environmental adaptation in the leathery sea squirt.