Structural, Evolutionary And Expression Analyses Of IRF1 Subfamily Genes Of Miiuy Croaker

Interferon(IFN) regulatory factors(IRFs) are a family of transcription factors, which were originally identified in the regulation of IFN expression; IRFs can regulate the IFN genes and IFN stimulated genes(ISGs), such as Mx, ISG15 and Vig-1. As critical transcription mediators, IRFs play important roles in antiviral defense, immune response, cell growth regulation and apoptosis and have been extensively investigated in mammals; however, in lower vertebrates have been rarely investigated. IRFs have also been widely studied in several fish species but not in miiuy croaker(Miichthys miiuy). Miiuy croaker, one representative species of the Sciaenidae family, is mainly distributed from the western Japan Sea to the East China Sea. In China, it is commercially important fish specie and has been widely cultured because of its abundant nutrients and medicinal value, but multiple viral pathogens have affected the aquaculture industry. IRF genes in fish should be better explored and comprehensive insights into the functions in the teleost immune system to improve fish health and increase the profits.The interferon regulatory factors IRF1 and IRF2 of the IRF1 subfamily play essential roles in immune responses against viruses. However, the structure and characteristics of IRF11 gene in fish have been rarely reported. In our study, IRF1, IRF2 and IRF11 genes were identified and characterized from miiuy croaker genome. Conducting bioinformatics analysis, we comprehensively evaluated IRF1, IRF2 and IRF11, including genomic organization, protein domain, gene synteny, molecular evolution, and expression profiles. We also analyzed IRF1 subfamily members in 1R?2R and 3R species, respectively to provide more information to analyze the evolution process of IRF1 subfamily.The ORFs of mmIRF1 was 900 bp. The multiple alignments of IRF1 genes from several species indicated that the IRF1 genes contained a conserved DBD with a motif composed of six conservative tryptophan residues. Miiuy croaker IRF1 exhibited a relatively high identity with the homologous proteins from other teleosts and the structure slightly differed from that of other fish. Gene synteny analysis results revealed that mmIRF1 exhibited a highly conserved synteny with other fish IRF1 except zebrafish. qRT-PCR was performed to investigate the expression patterns of IRF1 in miiuy croaker. In the uninfected group, miiuy croaker IRF1 was broadly expressed in liver, blood and intestines. Miiuy croaker IRF1 had high expression in the infected liver group and spleen group, but had a low expression in the infected kidney group. Evolutionary analysis showed one positive selection site in the mammalian IRF1 group, but no positive selection site in fish IRF1 group. IRF1 underwent different evolutionary patterns in mammals and fish.The mmIRF2 gene was 957 bp in length which coding a DBD with a motif composed of six conservative tryptophan residues. Bioinformatics analysis showed that miiuy croaker IRF2 share conserved gene structures and gene synteny with the IRF2 genes in other fish. Expression profiles analysis showed miiuy croaker IRF2 was broadly expressed in kidney in the uninfected group. And in the infected group, miiuy croaker IRF2 had high expression in the infected liver group and spleen group, but had a low expression in the infected kidney group. The evolutionary analysis showed mammalian IRF2 underwent the purifying selection, fish IRF2 genes underwent positive selection. IRF2 underwent different evolutionary patterns in mammals and fish, maybe caused because of the different environment.IRF11 is a novel IRF gene of the IRF1 subfamily; IRF11 genes share almost the same evolutionary distance with IRF1 and IRF2 genes. This study also confirmed that IRF11 is not specific to teleost fish; indeed, IRF11 is found not only in teleost fish but also in cartilaginous and coelacanth fishes. The miiuy croaker IRF1 was obtained from the genome and the full length is 900 bp. And miiuy croaker IRF11 contained a conserved DBD with a motif composed of six conservative tryptophan residues same as the other fish IRF11 genes. Also miiuy croaker had a relatively high identity with the homologous proteins from other teleosts. Bioinformatics analysis showed that miiuy croaker IRF11 share conserved gene structures and gene synteny with the IRF11 genes in other fish. Expression profiles analysis showed miiuy croaker IRF1 was broadly expressed in skin in the uninfected group. In the infected group, miiuy croaker IRF1 had high expression in the infected liver group and spleen group, but had a low expression in the infected kidney group. The evolutionary analysis showed IRF11 underwent the positive selection.