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Abstract Background Interferon regulatory factors (IRFs), which can be identified based on a unique helix-turn-helix DNA-binding domain (DBD) are a large family of transcription factors involved in host immune response, haemotopoietic differentiation and immunomodulation. Despite the identification of ten IRF family members in mammals, and some recent effort to identify these members in fish, relatively little is known in the composition of these members in other classes of vertebrates, and the evolution and probably the origin of the IRF family have not been investigated in vertebrates. Results Genome data mining has been performed to identify any possible IRF family members in human, mouse, dog, chicken, anole lizard, frog, and some teleost fish, mainly zebrafish and stickleback, and also in non-vertebrate deuterostomes including the hemichordate, cephalochordate, urochordate and echinoderm. In vertebrates, all ten IRF family members, i.e. IRF-1 to IRF-10 were identified, with two genes of IRF-4 and IRF-6 identified in fish and frog, respectively, except that in zebrafish exist three IRF-4 genes. Surprisingly, an additional member in the IRF family, IRF-11 was found in teleost fish. A range of two to ten IRF-like genes were detected in the non-vertebrate deuterostomes, and they had little similarity to those IRF family members in vertebrates as revealed in genomic structure and in phylogenetic analysis. However, the ten IRF family members, IRF-1 to IRF-10 showed certain degrees of conservation in terms of genomic structure and gene synteny. In particular, IRF-1, IRF-2, IRF-6, IRF-8 are quite conserved in their genomic structure in all vertebrates, and to a less degree, some IRF family members, such as IRF-5 and IRF-9 are comparable in the structure. Synteny analysis revealed that the gene loci for the ten IRF family members in vertebrates were also quite conservative, but in zebrafish conserved genes were distributed in a much longer distance in chromosomes. Furthermore, all ten different members are clustered in respectively different clades; but the IRF-11 was clustered with one in sea urchin. Conclusions In vertebrates, the ten well-characterized IRF family members shared a relatively high degree of similarity in genomic structure and syntenic gene arrangement, implying that they might have been evolved in a similar pattern and with similar selective pressure in different classes of vertebrates. Genome and/or gene duplication, and probably gene shuffling or gene loss might have occurred during the evolution of these IRF family members, but arrangement of chromosome or its segment might have taken place in zebrafish. However, the ten IRF family members in vertebrates and those IRF-like genes in non-vertebrate deuterostomes were quite different in those analyzed characters, as they might have undergone different patterns of evolution.

Background. Half-smooth tongue sole, Cynoglossus semilaevis Günther, 1873, a marine teleost, is an important aquaculture species of great economic value. In recent years, its farm production increase coincided, however, with the number of reported cases of bacterial diseases. Further understanding of its immune response to bacterial pathogens can provide more information on pathogenesis and how to prevent disease using immune-related strategy. Peptidoglycan (PGN) recognition proteins (PGRPs) play important roles in the innate immunity against bacterial infection. In the presently reported study, a long type PGRP in half-smooth tongue sole (csPGRP-L) was cloned, and its sequence features, PGN binding ability, and mRNA expressions in different tissues after bacterial infection were also analyzed. Materials and methods. The full length of csPGRP-L cDNA was obtained by RT-PCR and RACE-PCR method, and its sequence features were analyzed by multiple sequence alignment and phylogenetic tree. Meanwhile, its 3-D structure and PGN binding ability were analyzed by comparative modelling and molecular docking methods. Furthermore, the expressions of csPGRP-L in different tissues of healthy fish and fish infected with Streptococcus dysgalactiae were examined using quantitative real-time PCR method. Results. The full length of csPGRP-L cDNA was 1509 bp (GenBank accession No. HQ909441), with a 1446 bp of open reading frame (ORF) encoding 481 amino acids (aa), which possessed several conserved PGRP family features, e.g., a typical PGRP domain at its C-terminal, 3-D structure. Molecular docking showed that the csPGRP-L also possessed the PGN-binding ability. csPGRP-L was constitutive expressed in all the selected tissues from healthy fish and following S. dysgalactiae infection its expression was up-regulated in a tissue-specific expression pattern. Conclusion. The gene we cloned was exactly the homologue of vertebrates' long type PGRP in half-smooth tongue sole which was confirmed by several analyses and the up-regulation of csPGRP-L after bacterial infection suggest that csPGRP-L plays important role in antibacterial and anti-infective action. [ABSTRACT FROM AUTHOR]

Background: Interferon regulatory factors (IRFs), which can be identified based on a unique helix-turn-helix DNAbinding domain (DBD) are a large family of transcription factors involved in host immune response, haemotopoietic differentiation and immunomodulation. Despite the identification of ten IRF family members in mammals, and some recent effort to identify these members in fish, relatively little is known in the composition of these members in other classes of vertebrates, and the evolution and probably the origin of the IRF family have not been investigated in vertebrates. Results: Genome data mining has been performed to identify any possible IRF family members in human, mouse, dog, chicken, anole lizard, frog, and some teleost fish, mainly zebrafish and stickleback, and also in non-vertebrate deuterostomes including the hemichordate, cephalochordate, urochordate and echinoderm. In vertebrates, all ten IRF family members, i.e. IRF-1 to IRF-10 were identified, with two genes of IRF-4 and IRF-6 identified in fish and frog, respectively, except that in zebrafish exist three IRF-4 genes. Surprisingly, an additional member in the IRF family, IRF-11 was found in teleost fish. A range of two to ten IRF-like genes were detected in the non-vertebrate deuterostomes, and they had little similarity to those IRF family members in vertebrates as revealed in genomic structure and in phylogenetic analysis. However, the ten IRF family members, IRF-1 to IRF-10 showed certain degrees of conservation in terms of genomic structure and gene synteny. In particular, IRF-1, IRF-2, IRF-6, IRF-8 are quite conserved in their genomic structure in all vertebrates, and to a less degree, some IRF family members, such as IRF-5 and IRF-9 are comparable in the structure. Synteny analysis revealed that the gene loci for the ten IRF family members in vertebrates were also quite conservative, but in zebrafish conserved genes were distributed in a much longer distance in chromosomes. Furthermore, all ten different members are clustered in respectively different clades; but the IRF-11 was clustered with one in sea urchin. Conclusions: In vertebrates, the ten well-characterized IRF family members shared a relatively high degree of similarity in genomic structure and syntenic gene arrangement, implying that they might have been evolved in a similar pattern and with similar selective pressure in different classes of vertebrates. Genome and/or gene duplication, and probably gene shuffling or gene loss might have occurred during the evolution of these IRF family members, but arrangement of chromosome or its segment might have taken place in zebrafish. However, the ten IRF family members in vertebrates and those IRF-like genes in non-vertebrate deuterostomes were quite different in those analyzed characters, as they might have undergone different patterns of evolution. [ABSTRACT FROM AUTHOR]