Characterization, evolution, and expression analysis of TLR7 gene subfamily members in Mastacembelus armatus (Synbranchiformes: Mastacembelidae)

Molecular characterization and immune role of TLR7 in Labeo rohita

Background

Toll-like receptors (TLRs) play a vital role in the immune response by recognizing pathogen-associated molecular patterns (PAMPs) and triggering signaling pathways that activate innate immunity. In bony fish, TLR7 is essential for both antiviral and antibacterial defense; however, its interactions with a wide range of ligands and pathogens are still not well understood across various fish species. This study focuses on the identification and characterization of TLR7 in Labeo rohita (LrTLR7) and aims to evaluate its response to pathogen challenges and stimulation by PAMPs.

Methods

To clone the TLR7 gene, RNA was extracted from L. rohita kidney tissue using a standard protocol, followed by cDNA synthesis with commercial kits. The TLR7 gene was amplified by PCR, and the gel-purified product was cloned into the pGEM-T Easy vector. DNA sequencing and BLAST analysis confirmed the identity of the LrTLR7 gene. The ORF of LrTLR7 cDNA was predicted using ORF-finder, while structural motifs in the encoded protein were identified through SMART. Phylogenetic relationships were analyzed using MEGA7 to construct evolutionary trees. Gene expression profiles of LrTLR7 were evaluated by quantitative real-time PCR (qRT-PCR) across developmental stages, tissues/organs of rohu fingerlings, and during challenges with A, hydrophila and E. tarda infections, as well as LPS and Poly I:C stimulation. Mucosal RBCs and PBLs were isolated using density-gradient centrifugation with HiSep™ LSM 1077 (Himedia, India). Cultured L. rohita gill (LRG) cells in Leibovitz's L-15 medium were infected with A. hydrophila or E. tarda at a multiplicity of infection (MOI) of 1, following established protocols.

Results

LrTLR7 showed the closest phylogenetic affinity to TLR7 in Cyprinus carpio. During embryonic development, LrTLR7 expression surged dramatically (~111-fold, p<0.05) in embryos at 120 h post-fertilization (hpf). In L. rohita juveniles, the gene was ubiquitously expressed across tissues/organs, with peak expression in gills (~2,000-fold). Following infection with A. hydrophila or E tarda, LrTLR7 gene transcripts in the liver increased sharply at 6 hpi (~93-fold and ~53,000-fold, respectively). In the infected fish, mucosal RBCs showed a ~500,000-fold upregulation (p<0.05), while PBLs exhibited maximal responses at 24 hpi (~5,000-fold for A. hydrophila and ~10 million-fold for E. tarda). In the LRG cell line, LrTLR7 gene expression rose ~30-fold by 3 hpi. during A. hydrophila infection. In-vivo stimulation with LPS or poly I:C triggered a ~30,000-fold increase in hepatic LrTLR7 expression at 12 h post-stimulation, with kidney tissue showing secondary activation. Mucosal RBCs and PBLs displayed rapid (1-3 h) LrTLR7 upregulation following in-vitro ligand exposure. Imiquimod and gardiquimod activated LrTLR7-signalling pathways in both in-vivo and in-vitro systems, elevating transcription of IRF7 and type I interferon genes.

Conclusion

Similar to higher vertebrates, LrTLR7 plays a crucial role in responding to pathogenic invasions and various PAMPs to induce innate immunity. Consequently, TLR7 in fish represents a significant target for immune activation using specific agonists or ligands, which could aid in the prevention of fish diseases.

Molecular characterization and expression analysis of four toll-like receptors (TLR) genes: TLR2, TLR5S, TLR14 and TLR22 in Mastacembelus armatus under Aeromonas veronii infection

Toll-like receptors (TLRs) are important pattern recognition receptors that can recognize pathogen-associated molecular patterns (PAMPs), which in turn activate immune cells in vivo to perform immune functions. In this study, two TLR1 subfamily members (TLR2 and TLR14), one TLR5 subfamily member (TLR5S) and one TLR11 subfamily member (TLR22) genes were first identified in Mastacembelus armatus. In MaTLR2, MaTLR14 and MaTLR22, three main domains were identified, including leucine-rich repeat (LRR) domain, a transmembrane domain (TM) and an intracellular Toll/IL-1 receptor (TIR) domain as in most TLRs with no TM domain and TIR domain in MaTLR5S. The tissue expression of MaTLR2, MaTLR5S, MaTLR14 and MaTLR22 showed that they were ubiquitously expressed in all tested tissues. After infection with Aeromonas veronii, expression of MaTLR2, MaTLR14 and MaTLR22 was all downregulated in spleen and liver, but upregulated in kidney. By contrast, MaTLR5S showed upregulation in all three organs after bacterial infection. The amino acid sequence identity of MaTLR2 with other teleosts varied from 64.7% to 76.8%, while MaTLR5S exhibited a range of 70.9%-75.9%. MaTLR14 demonstrated a higher degree of similarity, with sequence identities ranging from 74% to 83.3%. In contrast, MaTLR22 showed the most variability, with sequence identities spanning from 42.5% to 74.6%. Phylogenetic analysis of TLR genes of M. aramatus clustered with Perciformes fishes, which aligned with traditional taxonomic classifications. The site model of PAML was used to detect the robust positively selected sites in extant teleost fishes. In total, 20, 12, 19 and 6 sites in the subsets of teleost TLR2, TLR5S, TLR14 and TLR22 were separately identified, indicating that the teleost TLR2, TLR5S, TLR14 and TLR22 had been subject to positive selection pressures. Our results will lay a good function for better understanding the potential function of TLRs in antibacterial process and their co-evolution with pathogens.

Transcriptome-wide identification and characterization of Toll pathway genes in Riptortus pedestris (Hemiptera: Alydidae)

The Toll pathway was first identified in Drosophila and plays an essential role in defense against infection by various pathogens. To date, various noncoding RNAs (ncRNAs) have been demonstrated to maintain immune homeostasis by regulating several target genes in the insect Toll pathway. However, the characterization and function of Toll pathway genes involved in the response to environmental changes at the posttranscriptional level associated with gut bacterial changes in Riptortus pedestris, which is a significant pest of soybeans, remain unclear. In this study, we identified and classified six Toll genes into three subtypes with typical Toll domain arrangements, including a Toll/interleukin receptor (TIR) domain, a transmembrane domain, and multiple leucine-rich repeat (LRR) domains; in addition, only one positive selection site was found in hemipteran sPP-Tolls, and a total of five downstream members in the Toll signaling pathway were selected and characterized. The expression patterns revealed that all these genes were widely expressed at all developmental stages of R. pedestris, and they presented variable expression levels among the different feeding treatments in the R. pedestris gut. Our comprehensive prediction analysis revealed that there are sixty miRNA‒mRNA interaction pairs, including fifty-six miRNA and six Toll pathway genes (P‒Toll1, sP‒Toll, Myd88, Pelle, Tube, and Cactus), and a ceRNA network comprising two lncRNA‒miRNA‒Toll pairs was constructed in response to environmental changes. Finally, the expression of some above genes and ncRNAs from the ceRNA network exhibited positive or negative association with the most changes in gut bacterial genera via Pearson correlation analysis. These findings provide valuable insights into how the Toll pathway of R. pedestris is involved in environmental adaptation at the posttranscriptional level and identifies new avenues for developing more effective methods for pest control through integration with gut bacteria.

Natural selection directing molecular evolution in vertebrate viral sensors

Diseases caused by pathogens contribute to molecular adaptations in host immunity. Variety of viral pathogens challenging animal immunity can drive positive selection diversifying receptors recognising the infections. However, whether distinct virus sensing systems differ across animals in their evolutionary modes remains unclear. Our review provides a comparative overview of natural selection shaping molecular evolution in vertebrate viral-binding pattern recognition receptors (PRRs). Despite prevailing negative selection arising from the functional constraints, multiple lines of evidence now suggest diversifying selection in the Toll-like receptors (TLRs), NOD-like receptors (NLRs), RIG-I-like receptors (RLRs) and oligoadenylate synthetases (OASs). In several cases, location of the positively selected sites in the ligand-binding regions suggests effects on viral detection although experimental support is lacking. Unfortunately, in most other PRR families including the AIM2-like receptor family, C-type lectin receptors (CLRs), and cyclic GMP-AMP synthetase studies characterising their molecular evolution are rare, preventing comparative insight. We indicate shared characteristics of the viral sensor evolution and highlight priorities for future research.

Molecular characterization and expression analysis of nine toll like receptor (TLR) genes in Scortum barcoo under Streptococcus agalactiae infection

Toll like receptors (TLRs) are important pattern recognition receptors participating in innate immune system. Up to now, no TLR has been identified in Jade perch (Scortum barcoo). In this study, we successfully identified 9 members of TLRs from the Jade perch. Amino acid sequence alignment analysis showed that the whole sequences of these TLRs were highly conserved among different fish species, especially in LRR, TM and TIR domains. Phylogenetic analysis revealed that each SbTLR was successfully grouped into corresponding gene family of teleosts. Expression analysis showed that most SbTLRs mainly expressed in liver, spleen, muscle and skin, while expressed less in brain and stomach. After Streptococcus agalactiae infection, expression of SbTLR2, SbTLR5S and SbTLR22 were significantly upregulated, while SbTLR3, SbTLR5M, SbTLR9, SbTLR13, and SbTLR14 were significantly downregulated. In all, this research first reported molecular characterization and expression profiles of 9 TLRs in Jade perch. These data will make a contribution for better understanding the antibacterial mechanism of TLRs in teleosts.

Genetic diversity of Toll-like receptor 9 in swamp eels (Monopterus albus)

The swamp eel, Monopterus albus, is an important aquaculture species in Asia (mainly China) whose production has seriously suffered from infectious diseases. In spite of the critical requirement for aquaculture practices, to date there is scant information on its immune defence. Here, the genetic characteristics of Toll-like receptor 9 (TLR9), which plays crucial roles in the initiation of host defence against microbial invasion, were analysed. It exhibits a striking lack of genetic variation resulting from a recent demographic bottleneck. A comparison with the homologue of M. javanensis revealed that replacement but not silent differences have nonrandomly accumulated in the coding sequences at the early stage following their split from a common ancestor. Furthermore, the replacements relevant to the type II functional divergence have mainly occurred in structural motifs mediating ligand recognition and receptor homodimerization. These results provide hints to understand the diversity-based strategy of TLR9 in the arms race against pathogens. Furthermore, the findings reported here give credence to the importance of basic immunology knowledge, especially for the key elements, in genetic engineering and breeding for disease resistance in the eel and other fishes.

Characterization and expression analysis of the interferon regulatory factor (IRF) gene family in zig-zag eel (Mastacembelus armatus) against Aeromonas veronii infection

Interferon regulatory factors (IRFs) play an important role in innate and adaptive immune system. However, in teleosts, the data on IRFs is still scarce. Here, for the first time, we identified 11 members of IRFs from the zig-zag eel Mastacembelus armatus (MarIRF1-10). The deduced protein sequences are highly conserved among different fish species especially in DBD and IAD domain. Phylogenetic analysis indicated that MarIRFs preferentially grouped with fish species in Synbranchiformes or Perciformes. Expression analysis showed that MarIRFs were expressed in all nine tissues including spleen, gill, muscle and intestine. After infected by Aeromonas veronii, expression of MarIRF2, MaIRF4b and MaIRF5 were significantly upregulated in spleen, MarIRF1, MarIRF2 were significantly upregulated in kidney, but in liver, nearly all MarIRFs were downregulated. Taken together, this study first reported molecular characterization and expression patterns of 11 IRFs in the zig-zag eel. All these results will contribute a lot to better understanding the antibacterial mechanism of IRFs in teleosts.

Characterization, evolution and expression analysis of Toll-like receptor 7 (TLR7) in turbot (Scophthalmus maximus L.)

The pattern recognition receptors (PRRs) can recognize the conserved molecular structures of pathogens to active the innate immune responses, and subsequently induce the antigen-specific adaptive immune responses for the clearance of infected pathogen. Among the PRRs, Toll-like receptors (TLRs) are the first and best characterized PRRs across all the species. Among the TLR members, TLR7 showed significant conservation across the vertebrates, with the lowest rate of evolution for its LRR domains from primates to fishes. In the current study, one TLR7 (SmTLR7) gene was captured in turbot, with a 3144 bp open reading frame (ORF), that encoding 1047 amino acid residues. Following multiple sequence comparison, SmTLR7 was found to have the highest similarity and identity both to Paralichthys olivaceus with 91.9% and 85.9%, respectively. In phylogenetic analysis, SmTLR7 was firstly clustered with Japanese flounder, and then clustered with fugu, rainbow trout, and zebrafish. In addition, SmTLR7 was widely expressed in all the examined tissues with the highest expression level in spleen, followed by skin, while the lowest expression level was detected in blood. Following both Edwardsiella tarda and Vibrio anguillarum challenge, SmTLR7 was significantly down-regulated in gill and intestine, and up-regulated in skin. Moreover, SmTLR7 was significantly up-regulated in head kidney macrophages following LPS, LTA, PGN and polyI:C stimulation, as well as showed the strongest binding ability to LPS, followed by PGN, LTA, and polyI:C in a dose-dependent manner. Finally, following RNAi of SmTLR7, MyD88 and IL-1β were slightly up-regulated, while TRAF6 and IL-8 were significantly down-regulated. The characterization of TLR7 can expand our understanding of the PRRs in teleost fishes, and eventually aid the exploration of interactions between host and pathogen.

Circadian clock components Bmal1 and Clock1 regulate tlr9 gene expression in the Japanese medaka (Oryzias latipes)

Currently, circadian regulation of immune molecules in lower vertebrates, particularly, diurnal oscillation in the immune status of a fish, is not well understood. In this study, the diurnal oscillation of toll-like receptor (Tlr) 9, which plays a role in pathogen recognition, was investigated in the Japanese medaka fish (Oryzias latipes). We confirmed the expression of tlr9 and clock genes (bmal1 and clock1) in the central and peripheral tissues of medaka. These genes were expressed in a diurnal manner in medaka acclimated to a 12-h:12-h light-dark (12:12 LD) cycle. In addition, increased tlr9 expression was detected in medaka embryo cells (OLHdrR-e3) overexpressing both bmal1 and clock1 genes; however, this result was not obtained when only one or neither of the genes was overexpressed. This suggests that the increase in expression was mediated by the Bmal1 and Clock1 proteins together. In vitro stimulation of the head kidney with CpG-oligodeoxynucleotides (CpG-ODNs) at different zeitgeber times (ZTs; ZT0 = light on, ZT12 = light off) affected the degree of tlr9 gene expression, showing high and low responsiveness to CpG-ODN stimulation at ZT6/10 and ZT18/22, respectively. Similarly, bacterial infection at different ZT points induced a difference in the expression of Tlr9 signaling pathway-related genes (tlr9 and myd88). These results suggested that fish tlr9 exhibits diurnal oscillation, which is regulated by clock proteins, and its responsiveness to immune-stimulation/pathogen infection depends on the time of the day.