Molecular characterization and expression analysis of TLR1 and TLR4 from the endangered fish Dabry's sturgeon (Acipenser dabryanus)

Characterization of TLR1 and expression profiling of TLR signaling pathway related genes in response to Aeromonas hydrophila challenge in hybrid yellow catfish (Pelteobagrus fulvidraco ♀ × P. vachelli ♂)

Toll‐like receptor 1 (TLR1) mediates the innate immune response to a variety of microbes through recognizing cell wall components (such as bacterial lipoproteins) in mammals. However, the detailed molecular mechanism of TLR1 involved in pathogen immunity in the representative hybrid yellow catfish (Pelteobagrus fulvidraco ♀ × P. vachelli ♂) has not been well studied. In the present study, we identified the TLR1 gene from the hybrid yellow catfish, and further comparative synteny data from multiple species confirmed that the TLR1 gene is highly conserved in teleosts. Phylogenetic analysis revealed distinguishable TLR1s in diverse taxa, suggesting consistence in evolution of the TLR1 proteins with various species. Structural prediction indicated that the three-dimensional structures of TLR1 proteins are relatively conserved among different taxa. Positive selection analysis showed that purifying selection dominated the evolutionary process of TLR1s and TLR1-TIR domain in both vertebrates and invertebrates. Expression pattern analysis based on the tissue distribution showed that TLR1 mainly transcribed in the gonad, gallbladder and kidney, and the mRNA levels of TLR1 in kidney were remarkably up-regulated after Aeromonas hydrophila stimulation, indicating that TLR1 participates in the inflammatory responses to exogenous pathogen infection in hybrid yellow catfish. Homologous sequence alignment and chromosomal location indicated that the TLR signaling pathway is very conserved in the hybrid yellow catfish. The expression patterns of TLR signaling pathway related genes (TLR1- TLR2 - MyD88 - FADD - Caspase 8) were consistent after pathogen stimulation, revealing that the TLR signaling pathway is triggered and activated after A. hydrophila infection. Our findings will lay a solid foundation for better understanding the immune roles of TLR1 in teleosts, as well as provide basic data for developing strategies to control disease outbreak in hybrid yellow catfish.

Computational analysis and functional characterisation of Tor putitora toll-like receptor 4 with the elucidation of its binding sites for microbial mimicking ligands

In the current study, full-length Toll-like receptor 4 (TLR4) cDNA was cloned and characterised in Tor putitora, an important fish inhibiting Himalayan rivers. The complete coding sequence of TpTLR4 is 2457 bp with nine key structural domains, including six leucine-rich repeats (LRRs). The phylogenetic tree revealed that TpTLR4 showed the closest relationship with TLR4 of Cyprinus carpio (96%), Labeo rohita (91%) and Megalobrama amblycephala (88%), all belonging to the Cyprinidae family. CELLO2GO tool revealed that TpTLR4 protein is highly localised in the plasma (67.7%), and the protein has a strong association with myeloid differentiation primary response 88 (MYD88) followed by Tumor necrosis factor receptor-associated factor (TRAF) family. In the toll-interleukin-1 receptor (TIR) domain of TpTLR4, the proline is replaced by the alanine amino acid, thus may give plasticity to the receptor to recognise both bacterial and viral ligands. Molecular docking has revealed that TpTLR4 showed the strongest affinity towards poly (I:C) with the binding energy of -6.1 kcal/mol and five hydrogen bonds among all ligands. Based on our molecular docking results, it can be presumed that TpTLR4 can sense bacterial, fungal and viral molecular patterns with binding sites mainly present in the TpTLR4 LRR9 motif, which spans between 515 and 602 amino acids. Tor putiora TLR4 transcript was ubiquitously expressed in all the tested fish tissues. Although, transcript level was found to be highest in blood and spleen followed by the kidney. The TpTLR4 transcripts showed peak expression in spleen and kidney at 12 h post-injection (hpi) (p < 0.05) of poly (I:C). The constitutive expression of TpTLR4 in various tissues, up-regulation in different tissues and strong binding affinities with poly (I:C) indicate that TpTLR4 may play an essential role in sensing pathogen-associated molecular patterns (PAMPs), particularly of viral origin.

Genome-wide identification and characterization of Toll-like receptor genes in black rockfish (Sebastes schlegelii) and their response mechanisms following poly (I:C) injection

Toll-like receptors (TLRs) are canonical transmembrane receptors that play an important role in defending against invading pathogens. In this study, we identified a total of 12 TLR genes in black rockfish (Sebastes schlegelii) with an analysis of their sequence characterizations. The phylogenetic analysis suggested that 12 distinct TLRs were grouped into five subfamilies (i.e., TLR1, TLR3, TLR5, TLR7, and TLR11 subfamilies), and each SsTLR gene respectively corresponded to the orthologs genes of other species. The protein domain analysis indicated that TLRs are type I transmembrane proteins, including an extracellular leucine-rich repeat (LRR), a transmembrane region (TM) domain and an intracellular Toll/IL-1 receptor (TIR) domain. The evolutionary ratios indicted that 12 SsTLRs were under purifying selection. qRT-PCR assays exhibited diverse TLRs molecular expression patterns in the heart, brain, head kidney, kidney, liver, intestine, and spleen of 3 black rockfish, and the expression levels were high in some immune tissues (e.g., head kidney, kidney, and spleen). Subsequently, 30 fish were equally divided into 2 groups i.e., poly (I:C)-treated and PBS-Control groups. After poly (I:C) injection, eight SsTLRs, i.e., SsTLR2, SsTLR2-1, SsTLR2-2, SsTLR3, SsTLR5S, SsTLR7, SsTLR8 and SsTLR22, were dramatically increased. Altogether these results contribute to understanding how SsTLRs respond to immune defense after poly (I:C) injection and provide researchers with comprehensive TLR gene family data of black rockfish.

TLR1 in Nile tilapia: The conserved receptor cannot interact with MyD88 and TIRAP but can activate NF-κB in vitro

Toll-like receptors (TLRs) play a critical role in the innate immune response of fish. In this study, we isolated the cDNA sequence of Nile tilapia TLR1 (OnTLR1). The deduced OnTLR1 protein contains a signal peptide, 7 leucine-rich repeats (LRRs), a C-terminal LRR (LRR-CT), a transmembrane region and a highly conserved TIR domain. In healthy Nile tilapia, the OnTLR1 transcript was broadly expressed in all examined tissues, with the highest expression levels in the spleen. After infection with Streptococcus agalactiae, the OnTLR1 transcripts were upregulated in the gill and kidney. After stimulation with polyinosinic-polycytidylic acid (poly(I:C)), the expression levels of OnTLR1 were significantly downregulated in the intestine, whereas OnTLR1 transcripts were significantly upregulated in the kidney. After challenge with lipopolysaccharide (LPS), the expression levels of OnTLR1 were significantly upregulated in the spleen and kidney. The subcellular localization showed that OnTLR1 was expressed in the cytoplasm. TLR1 significantly increased MyD88-dependent NF-κB activity. However, the results of a pull-down assay showed that OnTLR1 did not interact with MyD88 or TIRAP. Binding assays revealed the specificity of OnTLR1 for pathogen-associated molecular patterns (PAMPs) and bacteria that included S. agalactiae, Aeromonas hydrophila and poly(I:C) and LPS. Taken together, these findings suggest that OnTLR1, as a pattern recognition receptor (PRR), might play an important role in the immune response to pathogen invasion.

Cu/Zn Superoxide Dismutase and Catalase of Yangtze Sturgeon, Acipenser dabryanus: Molecular Cloning, Tissue Distribution and Response to Fasting and Refeeding

Superoxide dismutase and catalase are two major antioxidant enzymes in the fish antioxidant defense system, which can remove excess reactive oxygen species and protect fish from stress-induced oxidative damage. The present study aimed to clone the sequences of Yangtze sturgeon, Acipenser dabryanus, Cu/Zn superoxide dismutase (AdCu/Zn-SOD) and catalase (AdCAT), and to explore changes of gene expression in the liver and intestine during fasting and refeeding. A total of 120 fish were exposed to four fasting and refeeding protocols (fasting for 0, 3, 7, or 14 d and then refeeding for 14 d). The coding sequences of AdCu/Zn-SOD and AdCAT encoded 155 and 526 amino acid proteins, respectively, both of which were expressed mainly in the liver. During fasting, when compared to the control group, liver AdCu/Zn-SOD expression was significantly higher in the 3- and 14-d groups, whereas its intestinal expression increased significantly only in the 7-d group. Liver AdCAT expression increased significantly in the 3-, 7-, and 14-d groups. During refeeding, liver AdCu/Zn-SOD expression increased significantly in the 3-, 7-, and 14-d groups compared with those in the control group. Similarly, intestinal AdCu/Zn-SOD expression increased significantly in the 3- and 7-d groups. Moreover, intestinal AdCAT expression was significantly higher in the 3-d group than in the control group, but decreased significantly in the 14-d group. Our findings indicated that AdCu/Zn-SOD and AdCAT play important roles in protecting fish against starvation-induced oxidative stress. Yangtze sturgeon exhibited the potential to adapt to a starvation and refeeding regime.

Effects of a Potential Host Gut-Derived Probiotic, Bacillus subtilis 6-3-1, on the Growth, Non-specific Immune Response and Disease Resistance of Hybrid Grouper (Epinephelus fuscoguttatus♀ × Epinephelus lanceolatus♂)

A potential host-derived probiotic, Bacillus subtilis 6-3-1, was successfully screened from 768 isolates from the intestines of healthy hybrid grouper (Epinephelus fuscoguttatus ♀ × Epinephelus lanceolatus ♂) based on multiple probiotic characteristics in vitro assays, such as, non-hemolytic activity, extracellular enzyme activity, inhibitory activity against pathogens, tolerance to gastrointestinal stress, cell surface hydrophobicity, autoaggregation, and antibiotic susceptibility. Eight weeks of feeding trial revealed that dietary supplementation of B. subtilis 6-3-1 at all three concentrations (1 × 10⁶ CFU g^-1 as BS6; 1 × 10⁷ CFU g^-1 as BS7; 1 × 10⁸ CFU g^-1 as BS8) could promote the growth performance of hybrid groupers to a certain extent at different time points. At the end of 8th week, BS6 and BS8 significantly promoted the weight gain rate (WGR), specific growth rate (SGR) of hybrid groupers. The digestive enzyme activities were also increased in BS6 and BS8 groups comparing with those in control group, except that the increase of amylase activities in BS6 was not significant (P > 0.05). However, BS7 showed the best non-specific immunity stimulating effects among the three concentration groups. While BS7 significantly boosted serum total protein contents, lysozyme (LZM), total antioxidant capacity (T-AOC), superoxide dismutase (SOD), catalase (CAT), and acid phosphatase (ACP) levels, BS6 significantly enhanced serum total protein, LZM activity, and BS8 significantly improved LZM, respiratory bursts activity. B. subtilis 6-3-1 up-regulated the expression of MyD88 in head kidney and intestine and increased villi length (VL) in intestine of BS7 group. It also up-regulated the expression of IgM in head kidney in BS6 group and IgM and TLR1 in intestine of BS8 group. Though all B. subtilis 6-3-1 supplemented groups reduced the cumulative mortality rate post-Vibro harveyi-challenge, BS7 showed the best protection effects among the three concentration groups. In conclusion, with its immune promoting, intestine health enhancing, and V. harveyi resisting effects, BS7 show great potential to be used as a probiotic in hybrid grouper culture.

Molecular characterization and expression analysis of Tf_TLR4 and Tf_TRIL in yellow catfish Tachysurus fulvidraco responding to Edwardsiella ictaluri challenge

Toll-like receptors play significant roles in defensing against pathogen invasion. In this study, TLR4 and TRIL from Yellow catfish Tachysurus fulvidraco (Tf), were identified and characterized. The open reading frames of the Tf_TLR4 and Tf_TRIL genes were 2466 bp and 1827 bp in length, encoding 821 and 608 amino acids, respectively. The Tf_TLR4 consists of LRRs, a transmembrane domain and a TIR domain, and Tf_TRIL only contains LRRs and TIR domain. Homologous identity revealed that both Tf_TLR4 and Tf_TRIL have high protein sequence similarity with that of channel catfish Ictalurus punctatus. Both the Tf_TLR4 and Tf_TRIL genes were highly expressed in head kidney and brain, respectively. The mRNA expression levels of Tf_TLR4 and Tf_TRIL genes were up-regulated in intestine and immune-related tissues after challenge of Edwardsiella ictaluri. The microscopic observation of the gut showed that the pathological changes in midgut and hindgut are more obvious than that in foregut after challenged with E. ictaluri. These results indicate that these two genes play potential roles in the host defense against E. ictaluri invasion. This study will provide valuable information to better understand the synergistic roles of TLR4 and TRIL in the innate immune system of yellow catfish and other fish.

Grass carp (Ctenopharyngodon idella) IRAK1 and STAT3 up-regulate synergistically the transcription of IL-10

In vertebrates, IL-10 is an anti-inflammatory factor that serves as a key inhibitory role in a wide range of immune responses. IRAK1 (IL-1 receptor-associated kinase 1), a key molecule in the inflammatory signal of IL-1R/TLR, plays an important pivotal role in regulating the autoimmunity of body. STAT3 (Signal transducer and activator of transcription 3) activated by IRAK1 participates in inflammation, tumorigenesis, metabolic disorders and immune response. Under the stimulation of LPS, IRAK1 enters the nucleus to form a dimer with STAT3 and regulates the expression of IL-10. However, the relationship between fish IRAK1 and STAT3 has not been reported. To explain the anti-inflammation in fish, we amplified and identified the complete open reading frame of grass carp IRAK1 (CiIRAK1) and STAT3 (CiSTAT3) based on the existing sequences. The expression of CiIRAK1 and CiSTAT3 were up-regulated significantly under the stimulation of LPS. This result suggests that both CiIRAK1 and CiSTAT3 may be involved in LPS-induced TLR4 pathway. The subcellular localization experiment revealed that CiIRAK1 is distributed in cytoplasm and enters nucleus after LPS stimulation. CiSTAT3 is distributed in both cytoplasm and nucleus with or without LPS stimulation. Immunoprecipitation assay revealed that CiIRAK1 interacted with CiSTAT3 under LPS stimulation. However in absence of LPS stimulation, CiIRAK1 and CiSTAT3 cannot interact with each other. Subsequently, immunofluorescence colocalization experiment further proved the interaction of CiIRAK1 and CiSTAT3 in nucleus under LPS stimulation. The dual luciferase reporter assays indicated that the binding of CiIRAK1 and CiSTAT3 synergistically enhanced the activity of CiIL-10 promoter.

Grass carp (Ctenopharyngodon idellus) TRAF6 up-regulates IFN1 expression by activating IRF5

In mammals, interferon regulatory factor 5 (IRF5) can be activated by tumor necrosis factor receptor-associated factor 6 (TRAF6). Upon activation, IRF5 translocates into the nucleus, where it binds to IFN promoter and up-regulates IFN expression. However, there are few reports on the molecular mechanism by which TRAF6 up-regulates IFN expression in fish. In this study, we explored how Grass carp (Ctenopharyngodon idellus) TRAF6 initiated innate immunity by activating IRF5. We found that CiTRAF6, CiIRF5 and CiIFN1 were all significantly up-regulated in LPS-stimulated CIK cells and the expression of CiTRAF6 was earlier than the expressions of CiIRF5 and CiIFN1. These findings suggested that CiIFN1 expression might be induced by CiTRAF6 in fish. CiIFN1 expression, CiIFN1 promoter activity and CO cells viability were all significantly up-regulated in the overexpression experiments, but they were significantly down-regulated in the gene silencing experiments. This indicated that CiTRAF6, along with CiIRF5, regulated CiIFN1 expression. The localization analysis found that both CiTRAF6 and CiIRF5 located in the cytoplasm. Following LPS stimulation, CiIRF5 was observed to translocate to the nucleus. GST-pull down and co-IP experiments revealed that CiTRAF6 interacted with CiIRF5. The colocalization analysis also showed that CiTRAF6 bound with CiIRF5 in the cytoplasm. Overexpression of CiTRAF6 increased the endogenous CiIRF5, promoted its ubiquitination and nuclear translocation. In conclusion, CiTRAF6 bound to CiIRF5 in the cytoplasm, and then activated CiIRF5, resulting in up-regulating the expression of CiIFN1.

In vitro immune response of chinook salmon (Oncorhynchus tshawytscha) peripheral blood mononuclear cells stimulated by bacterial lipopolysaccharide

We investigated cellular functional and targeted immune cytokine responses of farmed Chinook salmon (Oncorhynchus tshawytscha) peripheral blood mononuclear cells (PBMCs) in vitro to LPS from Escherichia coli (E. coli) serotypes O111: B4 and O55: B5, and a phorbol ester phorbol 12-myristate 13-acetate (PMA). Bacterial LPS and PMA significantly (p < 0.05) induced reactive oxygen species (ROS) production in O. tshawytscha PBMCs, and enhanced by interferon (IFN)-inducible cytokine production. Cellular phagocytosis was significantly enhanced with PMA and E. coli serotype O111: B4 LPS after 1 and 2 h respectively. At the molecular level, LPS and PMA significantly (p < 0.05) upregulated pro-inflammatory cytokine gene transcripts for IFNγ, TNF-α, and anti-inflammatory IL-10, 24 h post-stimulation. This response is postulated to be mediated via the MyD88 and TRIF pathways in TLR4, or synergistic TLR1 and TLR2 receptors. This is the first report of LPS induced immune related in vitro responses in farmed O. tshawytscha PBMCs.

A Comparison of the Innate and Adaptive Immune Systems in Cartilaginous Fish, Ray-Finned Fish, and Lobe-Finned Fish

The immune system is composed of two subsystems-the innate immune system and the adaptive immune system. The innate immune system is the first to respond to pathogens and does not retain memory of previous responses. Innate immune responses are evolutionarily older than adaptive responses and elements of innate immunity can be found in all multicellular organisms. If a pathogen persists, the adaptive immune system will engage the pathogen with specificity and memory. Several components of the adaptive system including immunoglobulins (Igs), T cell receptors (TCR), and major histocompatibility complex (MHC), are assumed to have arisen in the first jawed vertebrates-the Gnathostomata. This review will discuss and compare components of both the innate and adaptive immune systems in Gnathostomes, particularly in Chondrichthyes (cartilaginous fish) and in Osteichthyes [bony fish: the Actinopterygii (ray-finned fish) and the Sarcopterygii (lobe-finned fish)]. While many elements of both the innate and adaptive immune systems are conserved within these species and with higher level vertebrates, some elements have marked differences. Components of the innate immune system covered here include physical barriers, such as the skin and gastrointestinal tract, cellular components, such as pattern recognition receptors and immune cells including macrophages and neutrophils, and humoral components, such as the complement system. Components of the adaptive system covered include the fundamental cells and molecules of adaptive immunity: B lymphocytes (B cells), T lymphocytes (T cells), immunoglobulins (Igs), and major histocompatibility complex (MHC). Comparative studies in fish such as those discussed here are essential for developing a comprehensive understanding of the evolution of the immune system.

Transcriptome analysis of the critically endangered Dabry's sturgeon (Acipenser dabryanus) head kidney response to Aeromonas hydrophila

Dabry's sturgeon (Acipenser dabryanus), as a living fossil, is considered a critically endangered aquatic animal in China. To date, the immune system of this species remains largely unknown, with limited available sequence information. In addition, increasing incidence of bacterial pathogenic diseases has been reported. Hence, the present study aimed to characterize comprehensively transcriptome profile of the head kidney from Dabry's sturgeon infected with Aeromonas hydrophila using Illumina platform. Over 42 million high-quality reads were obtained and de novo assembled into a final set of 195240 unique transcript fragments (unigenes), with an average length of 564 bp. Approximately 41702 unigenes were annotated in the NR NCBI database. Dabry's sturgeon unigenes had the highest number of hits with 14365 (34.45%) to Lepisosteus oculatus. The 195240 unigenes were assigned to three Gene Ontology (GO) categories: biological process, cellular component, and molecular function. Among them, 27770 unigenes were clustered into 26 Eukaryotic Orthologous Group (KOG) functional categories, and 36031 unigenes were mapped to 335 known Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. After A. hydrophila administration, 1728 differentially expressed unigenes were identified, including 980 upregulated and 748 downregulated unigenes. Further KEGG enrichment analysis of these unigenes identified 16 immune-related pathways, including the Toll-like receptor signaling pathway, chemokine signaling pathway, complement and coagulation pathway, RIG-I-like receptor signaling pathway, and NOD-like receptor signaling pathway. 20 DEGs were selected and their expression patterns are largely consistent with the transcriptome profile analysis, which clearly validated the reliability of the DEGs in transcriptome analysis. This work revealed novel gene expression patterns of Dabry's sturgeon host defense and contributes to a better understanding of the immune system and defense mechanisms of Dabry's sturgeon in response to bacterial infection. The results provide valuable references for studies in sturgeons that lack complete genomic sequences, and could also be helpful for the analyzing evolution among cartilaginous and teleost fish.