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 alpha-helices and beta-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 doublestrand 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 WSSVinfected 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.

Automated summary

This study analyzed the transcriptome and proteome profiles of shrimp infected with WSSV after knocking down PvIRF using RNA sequencing and isobaric tags for relative and absolute quantification. The results showed that PvIRF is involved in inhibiting the replication of WSSV in shrimp and may participate in IRF-mediated interferon regulation through JAK/STAT and Toll signaling pathways.