Gene cloning and expression analysis of IRF1 in half-smooth tongue sole (Cynoglossus semilaevis)

Functional Analysis of IRF1 Reveals its Role in the Activation of the Type I IFN Pathway in Golden Pompano, Trachinotus ovatus (Linnaeus 1758)

Interferon (IFN) regulatory factor 1 (IRF1), a transcription factor with a novel helix–turn–helix DNA-binding domain, plays a crucial role in innate immunity by regulating the type I IFN signaling pathway. However, the regulatory mechanism through which IRF1 regulates type I IFN in fish is not yet elucidated. In the present study, IRF1 was characterized from golden pompano, Trachinotus ovatus (designated ToIRF1), and its immune function was identified to elucidate the transcriptional regulatory mechanism of ToIFNa3. The full-length complementary DNA (cDNA) of IRF1 is 1763 bp, including a 900-bp open reading frame (ORF) encoding a 299-amino-acid polypeptide. The putative protein sequence has 42.7–71.7% identity to fish IRF1 and possesses a representative conserved domain (a DNA-binding domain (DBD) at the N-terminus). The genomic DNA sequence of ToIRF1 consists of eight exons and seven introns. Moreover, ToIRF1 is constitutively expressed in all examined tissues, with higher levels being observed in immune-relevant tissues (whole blood, gill, and skin). Additionally, Cryptocaryon irritans challenge in vivo increases ToIRF1 expression in the skin as determined by Western blotting (WB); however, protein levels of ToIRF1 in the gill did not change significantly. The subcellular localization indicates that ToIRF1 is localized in the nucleus and cytoplasm with or without polyinosinic/polycytidylic acid (poly (I:C)) induction. Furthermore, overexpression of ToIRF1 or ToIFNa3 shows that ToIRF1 can notably activate ToIFNa3 and interferon signaling molecule expression. Promoter sequence analysis finds that several interferon stimulating response element (ISRE) binding sites are present in the promoter of ToIFNa3. Additionally, truncation, point mutation, and electrophoretic mobile shift (EMSA) assays confirmed that ToIRF1 M5 ISRE binding sites are functionally important for ToIFNa3 transcription. These results may help to illuminate the roles of teleost IRF1 in the transcriptional mechanisms of type I IFN in the immune process.

Identification and characterization of interferon regulatory factor 1 from Lateolabrax japonicus involved in antiviral immune response against grouper nervous necrosis virus infection

Interferon regulatory factors (IRFs) play a key role in mediating the host response against pathogen infection and other important biological processes. In the present study, an interferon regulation factor 1 gene was identified from Lateolabrax japonicus (designated LjIRF-1), the cDNA sequence of LjIRF-1 was 1394 bp long, and with an open reading frame (ORF) of 945 bp that encodes a peptide of 314 amino acids. Bioinformatics data showed that LjIRF-1 possesses a DNA-binding domain (DBD) and two low complexity regions, which shared 56-81% identity to other fish IRF-1s. The LjIRF-1 transcripts were detectable in all examined tissues of healthy L. japonicus, with higher levels in the blood, head-kidney, intestine, gill and spleen. When challenged with grouper nervous necrosis virus (GNNV) and poly (I:C) infection, both the mRNA expression levels of LjIRF-1 and L. japonicus interferon-1 gene (designated LjIFN-1) were significantly up-regulated. Furthermore, like with poly (I:C), the active purified recombinant protein (rLjIRF-1) was also capable of increasing the expression level of LjIFN-1; controlling the copy number of GNNV under lethiferous titer (10¹¹-10¹² copies/μL) and promoting the survival rate of GNNV infected L. japonicas. Combine all the results, we deduced that LjIRF-1 is involved in defending GNNV infection by simulating LjIFN-1 signal pathway in L. japonicas.

First Study on Interferon Regulatory Factor in Sturgeon: Expression Pattern of Interferon Regulatory Factor in Dabry's Sturgeon Acipenser dabryanus

Interferon regulatory factors (IRFs) are crucial regulators in initiating the host innate immune response against pathogen invasions. Dabry's sturgeon (Acipenser dabryanus) is particularly a valuable fish species found in the Yangtze River, China for which there is scarce immunological data. In the present study, we investigated the expression profile of sturgeon IRF genes. All adIRFs were composed of 8 exons and 7 introns, except adIRF1, which possessed 9 exons interrupted by 8 introns. Moreover, the predicted protein sequence has a DNA-binding domain (DBD) sharing high identity with spotted gar (Lepisosteus oculatus). Regarding the expression patterns, 5 adIRF genes were found to be constitutively expressed in all tissues examined, and were significantly higher in lymphoid organs (eg, blood, kidney, intestine, and spleen). Following Aeromonas hydrophila infection, the expression of adIRF1 and adIRF3 were upregulated in the spleen and caudal kidney, while both the adIRF5 and adIRF8 genes were downregulated in caudal kidney. In addition, adIRF4 was significantly upregulated at 3 h postinfection by A. hydrophila in the spleen and caudal kidney. These results suggest that adIRFs are related to the immune response to bacterial infection, which will help clarify the function of these IRFs and provide a fundamental basis for protecting the Dabry's sturgeon.

Characterization of the gilthead seabream (Sparus aurata L.) immune response under a natural lymphocystis disease virus outbreak

Lymphocystis or lymphocystis disease virus (LCDV) is distributed worldwide and affects many fresh and marine water fish species. LCDV is commonly found in aquaria fish species but also in farmed fish species, among them the gilthead seabream (Sparus aurata L.). The immune status of gilthead seabream (S. aurata) specimens under a natural outbreak of LCDV was studied. The replication of the virus was demonstrated in infected fish, but not in control fish. The results showed decreased total serum IgM levels and increased innate cellular immune response (peroxidase and respiratory burst activities) of head kidney leucocytes in LCDV-infected fish, compared to the values obtained in uninfected specimens. In addition, transcription of antiviral genes (ifn and irf3) was down-regulated in the skin of LCDV-positive fish as well as genes involved in cellular immunity (csf1r, mhc2a, tcra and ighm) that were down-regulated in skin and head kidney of infected fish. By contrast, the transcription of nccrp1 was up-regulated in head kidney after LCDV infection. These present results show that head kidney leucocytes are activated to encounter the virus at the sites of replication.

Molecular identification and functional characterisation of the interferon regulatory factor 1 in the blunt snout bream (Megalobrama amblycephala)

Interferon regulatory factors (IRFs) play a key role in mediating the host response against pathogen infection and other important biological processes. This is the first report of an IRF family member in blunt snout bream Megalobrama amblycephala. The complete cDNA of M. amblycephala (Ma) IRF1 gene has 1422 nucleotides (nt.), with an open reading frame of 858 nt, encoding a polypeptide of 285 amino acids. The putative MaIRF1 polypeptide shared significant structural homology with known IRF1 homologs: a conserved IRF domain was found at the N-terminal and an IRF association domain 2 at the C-terminal. Phylogenetic analysis showed that MaIRF1 amino acid sequence clustered with other teleost IRF1s, with a grass carp ortholog exhibiting the highest similarity. MaIRF1 mRNA expression patterns were studied using quantitative real-time PCR in healthy fish tissues and after a challenge with Aeromonas hydrophila bacterium. It was constitutively expressed in all examined tissues: the highest in blood, the lowest in muscle. The expression after A. hydrophila challenge was up-regulated in liver, spleen and kidney, but down-regulated in intestine and gills. At the protein level, similar expression patterns were observed in liver and gills. Patterns differed in intestine (up-regulation), spleen (down-regulation) and kidney (expression mostly unchanged). This study indicates that MaIRF1 gene plays an important role in the blunt snout bream immune system, hence providing an important base for further studies.

Expression profile of carp IFN correlate with the up-regulation of interferon regulatory factor-1 (IRF-1) in vivo and in vitro: the pivotal molecules in antiviral defense

Interferon regulatory factors (IRFs) are a family of transcription factors that mediate the transcriptional regulation of interferon (IFN) genes and IFN-inducible genes. In this study, IRF-1 gene is cloned from the common carp, Cyprinus carpio L., named CcIRF-1. The full-length cDNA of CcIRF-1 is 1427 bp, including an open reading frame of 861 bp encoding a protein of 286 amino acids. The putative CcIRF-1 is characterized by a conserved DNA-binding domain and includes a signature of six conserved tryptophan residues. The genomic sequence of CcIRF-1 is described, which consists of 9 exons and 8 introns. The sequence analysis shows that CcIRF-1 is clustered into IRF-1 subfamily, and has the closest relationship with the zebrafish IRF-1. CcIRF-1 is found constitutively expressed in different organs of healthy common carp. The main findings are that CcIRF-1 is up-regulated following stimulation with poly(I:C) in all tested tissues. Moreover, the downstream gene of IRF-1 - IFN is found to be correlated with the up-regulation of IRF-1 after injection with poly(I:C). Furthermore, we also isolate the peripheral blood leukocytes (PBLs) and find that there is a relevance between the expression profile of CcIRF-1 and IFN in poly(I:C) stimulated PBLs.

Complement factor I from flatfish half-smooth tongue (Cynoglossus semilaevis) exhibited anti-microbial activities

Complement factor I (Cfi) is a soluble serine protease which plays a crucial role in the modulation of complement cascades. In the presence of substrate modulating cofactors (such as complement factor H, C4bp, CR1, etc), Cfi cleaves and inactivates C3b and C4b, thereby controlling the complement-mediated processes. In this study, we sequenced and characterized Cfi gene from Cynoglossus Semilaevis (designated as CsCfi) for the first time. The full-length cDNA of CsCfi was 2230 bp in length, including a 98 bp 5'-untranslated region (UTR), a 164 bp 3'-UTR and a 1968 bp open reading frame (ORF). It encoded a polypeptide of 656 amino acids, with a molecular mass of 72.28 kDa and an isoelectric point of 7.71. A signal peptide was defined at N-terminus, resulting in a 626-residue mature protein. Multiple sequence alignment revealed that Cfi proteins were well conserved with the typical modular architecture and identical active sites throughout the vertebrates, which suggested the conserved function of Cfi. Phylogenetic analysis indicated that CsCfi and the homologous Cfi sequences from teleosts clustered into a clade, separating from another clade from the cartilaginous fish and other vertebrates. Tissue expression profile analysis by quantitative real-time PCR (qRT-PCR) showed that CsCfi mRNA constitutively expressed in all tested tissues, with the predominant expression in liver and the lowest in stomach. Temporal expression levels of CsCfi after challenging with Vibrio anguillarum showed different expression patterns in intestine, spleen, skin, blood, head kidney and liver. The recombinant CsCfi (rCsCfi) protein showed broad-spectrum antimicrobial activities against the Gram-positive bacteria Staphylococcus aureus and the Gram-negative bacteria Escherichia coli, Pseudomonas aeruginosa and Shewanella putrefaciens. The research revealed that CsCfi plays an important role in C. Semilaevis immunity.

Molecular characterization and expression analysis of eleven interferon regulatory factors in half-smooth tongue sole, Cynoglossus semilaevis

Interferon regulatory factors (IRFs) act as transcription mediators in virus-, bacteria-, and interferon (IFN)-induced signaling pathways and play diverse functions in antimicrobial defense, immune modulation, hematopoietic differentiation, and cell apoptosis. In this study, we described for the first time eleven IRFs (IRF1, IRF1L, IRF2X1, IRF3, IRF4a, IRF4b, IRF5, IRF6, IRF7, IRF8, and IRF9) from half-smooth tongue sole (Cynoglossus semilaevis) and examined their tissue distributions and expression patterns under different conditions. The deduced protein sequences of these IRFs (except IRF1) share high identities (71.8-86.6%) with other corresponding IRFs in other teleosts, whereas the sequence identity of IRF1 with the corresponding IRF1 in other teleosts is only 58.1%. A conserved N-terminal DNA binding domain (DBD), which is characterized by a winged type helix-loop-helix motif with four to six tryptophan repeats, is present in all IRFs. Another conserved IRF associated domain (IAD), which mediates the interactions in the C-terminal part of the protein, is present in all IRFs except IRF1 and IRF2X1, which instead contain the IAD2 domain. Several special domains also were found, including a serine-rich domain (SRD) in IRF3, IRF4a, IRF4b, and IRF7; a proline-rich domain (PRD) in IRF9; nuclear localization signals (NLSs) in IRF5, IRF8, and IRF9; and a virus activated domain (VAD) in IRF5. Quantitative real time RT-PCR (qRT-PCR) analysis showed that expression of all IRFs occurred in multiple tissues. IRF1, IRF2X1, IRF4a, IRF5, IRF7, and IRF8 exhibited relatively high levels of expression in immune organs, whereas the other five IRFs displayed high levels of expression in non-immune organs. Infection with extracellular and intracellular bacterial pathogens and virus upregulated the expression of IRFs in a manner that depended on tissue type, pathogen, and infection stage. Specifically, IRF1 and IRF2X1 were highly induced by bacterial and viral pathogens; IRF1L and IRF6 responded mainly to extracellular and intracellular bacterial pathogens; IRF3, IRF5, IRF7, IRF8, and IRF9 were markedly induced by intracellular bacterial pathogen and virus; IRF4a and IRF4b were mainly induced by virus and intracellular bacterial pathogen respectively. These results indicate that the IRFs of C. semilaevis can be categorized into several groups which exhibit different expression patterns in response to the infection of different microbial pathogens. These results provide new insights into the roles of teleost IRFs in antimicrobial immunity.

Antibacterial products of marine organisms

Marine organisms comprising microbes, plants, invertebrates, and vertebrates elaborate an impressive array of structurally diverse antimicrobial products ranging from small cyclic compounds to macromolecules such as proteins. Some of these biomolecules originate directly from marine animals while others arise from microbes associated with the animals. It is noteworthy that some of the biomolecules referred to above are structurally unique while others belong to known classes of compounds, peptides, and proteins. Some of the antibacterial agents are more active against Gram-positive bacteria while others have higher effectiveness on Gram-negative bacteria. Some are efficacious against both Gram-positive and Gram-negative bacteria and against drug-resistant strains as well. The mechanism of antibacterial action of a large number of the chemically identified antibacterial agents, possible synergism with currently used antibiotics, and the issue of possible toxicity on mammalian cells and tissues await elucidation. The structural characteristics pivotal to antibacterial activity have been ascertained in only a few studies. Demonstration of efficacy of the antibacterial agents in animal models of bacterial infection is highly desirable. Structural characterization of the active principles present in aqueous and organic extracts of marine organisms with reportedly antibacterial activity would be desirable.