Molecular Characterization and Evolution Analysis of Two Forms of TLR5 and TLR13 Genes Base on Larimichthys crocea Genome Data

Riding the wave of innovation: immunoinformatics in fish disease control

The spread of infectious illnesses has been a significant factor restricting aquaculture production. To maximise aquatic animal health, vaccination tactics are very successful and cost-efficient for protecting fish and aquaculture animals against many disease pathogens. However, due to the increasing number of immunological cases and their complexity, it is impossible to manage, analyse, visualise, and interpret such data without the assistance of advanced computational techniques. Hence, the use of immunoinformatics tools is crucial, as they not only facilitate the management of massive amounts of data but also greatly contribute to the creation of fresh hypotheses regarding immune responses. In recent years, advances in biotechnology and immunoinformatics have opened up new research avenues for generating novel vaccines and enhancing existing vaccinations against outbreaks of infectious illnesses, thereby reducing aquaculture losses. This review focuses on understanding in silico epitope-based vaccine design, the creation of multi-epitope vaccines, the molecular interaction of immunogenic vaccines, and the application of immunoinformatics in fish disease based on the frequency of their application and reliable results. It is believed that it can bridge the gap between experimental and computational approaches and reduce the need for experimental research, so that only wet laboratory testing integrated with in silico techniques may yield highly promising results and be useful for the development of vaccines for fish.

Transcriptome-wide analyses of early immune responses in lumpfish leukocytes upon stimulation with poly(I:C)

Background

Both bacterial and viral diseases are a major threat to farmed fish. As the antiviral immune mechanisms in lumpfish (Cyclopterus lumpus L.) are poorly understood, lumpfish leukocytes were stimulated with poly(I:C), a synthetic analog of double stranded RNA, which mimic viral infections, and RNA sequencing was performed.

Methods

To address this gap, we stimulated lumpfish leukocytes with poly(I:C) for 6 and 24 hours and did RNA sequencing with three parallels per timepoint. Genome guided mapping was performed to define differentially expressed genes (DEGs).

Results

Immune genes were identified, and transcriptome-wide analyses of early immune responses showed that 376 and 2372 transcripts were significantly differentially expressed 6 and 24 hours post exposure (hpe) to poly(I:C), respectively. The most enriched GO terms when time had been accounted for, were immune system processes (GO:0002376) and immune response (GO:0006955). Analysis of DEGs showed that among the most highly upregulated genes were TLRs and genes belonging to the RIG-I signaling pathway, including LGP2, STING and MX, as well as IRF3 and IL12A. RIG-I was not identified, but in silico analyses showed that genes encoding proteins involved in pathogen recognition, cell signaling, and cytokines of the TLR and RIG-I signaling pathway are mostly conserved in lumpfish when compared to mammals and other teleost species.

Conclusions

Our analyses unravel the innate immune pathways playing a major role in antiviral defense in lumpfish. The information gathered can be used in comparative studies and lay the groundwork for future functional analyses of immune and pathogenicity mechanisms. Such knowledge is also necessary for the development of immunoprophylactic measures for lumpfish, which is extensively cultivated for use as cleaner fish in the aquaculture for removal of sea lice from Atlantic salmon (Salmo salar L.).

Recombinant Vibrio harveyi flagellin A protein and partial deletions of middle variable region and D0 domain induce immune related genes in Epinephelus coioides and Cyprinus carpio

Vibrio harveyi is a Gram-negative bacterium that causes vibriosis in various aquaculture species, including the orange-spotted grouper (Epinephelus coioides). Bacterial flagellin is a potent pathogen-associated molecule that stimulates the innate and adaptive immune systems through toll-like receptor 5 (TLR5) signaling. In this study, we isolated V. harveyi flagellin A (VhFliA) gene from V. harveyi (originated from orange-spotted grouper) and investigated the in vivo activities of recombinant VhFliA protein. Multiple sequence alignment showed that the amino acid sequence of VhFliA has conserved domains of N- and C-terminals (D0 and D1) and a middle variable (MV) region. We produced the VhFliA recombinant protein (wild type (WT)-VhFliA) by Escherichia coli and investigated its in vivo biological activity. Additionally, we prepared the VhFliA recombinant proteins with deletion of domains (ΔMV-VhFliA and ΔD0MV-VhFliA) to identify the domain for biological activity in the orange-spotted grouper. WT and ΔMV-VhFliA induced the expression of inflammatory cytokines (IFNγ, IL-1β, and IL-8) in groupers. However, ΔD0MV-VhFliA did not induce the expression of inflammatory cytokines. Additionally, to demonstrate the applicability of recombinant VhFliA to teleost species, we performed an in vivo assay of the recombinant proteins in koi carp (Cyprinus carpio). WT-VhFliA stimulates the expression of inflammatory cytokines (IL-1β, IL-6, and IL-8) in carp. ΔMV-VhFliA did not upregulate IL-1β and IL-6, whereas ΔD0MV-VhFliA induced expression in carp. These findings showed the potential of VhFliA as an effective immune stimulant adjuvant and comparative studies of flagellin - TLR5 signaling in teleosts.

Characterization of a novel Toll-like receptor 13 homologue from a marine fish Nibea albiflora, revealing its immunologic function as PRRs

Congenital immunity mediated by Toll-like receptor (TLR) family is the first line of defense for disease-resistant immunity of fish and plays a vital role as a bridge between innate immunity and acquired immunity. As a less known member of the TLR family TLR13 can participate in the immune and inflammatory reactions of the body for recognizing the conserved sequence of 23S rRNA in bacteria and induce immune response. In this study, the full-length cDNA of TLR13 from Nibea albiflora (named as NaTLR13) was cloned and was functionally characterized. It was 4210bp (GenBank accession no. MT701899) including an open reading frame (ORF) of 2886bp to encode 962 amino acids with molecular weight of 110.37 kDa and the theoretical isoelectric point of 9.08. There were several conservative structures in NaTLR13 such as 15 leucine-rich repeat sequences (LRRs), a Toll-IL-1 receptor domain (TIR), an LRR-CT terminal domain, two LRR-TYP structures and two transmembrane domains. The multiple sequence alignment and phylogenetic analysis manifested that NaTLR13 had high similarity with Larimichthys crocea and Collichthys lucidus (88.79% and 87.02%, respectively) and they fell into the same branch. The Real-time PCR showed that NaTLR13 was expressed in all selected tissues, with the highest in the spleen, followed by the liver, kidney, gill, heart and muscle. After being challenged by Vibrio alginolyticus, Vibrio parahaemolyticus or Poly (I:C), the expression of NaTLR13 increased firstly, then decreased and finally stabilized with time for its immune defense function. Subcellular localization analysis revealed that NaTLR13 was unevenly distributed in the cytoplasm with green fluorescence and MyD88 was evenly spread in the cytoplasm with red signals. When NaTLR13 and MyD88 were co-transfected, they obviously overlapped and displayed orange-yellow color, which showed that the homologous TLR13 might interact with MyD88 for NFκB signaling pathway transmission. The functional domains of NaTLR13 (named NaTLR13-TIR and NaTLR13-LRR) were expressed in E.coli BL21 (DE3) and purified by Ni-NAT Superflow Resin conforming to the expected molecular weights, and the recombinant proteins could bind to three Vibrios (V.alginolyticus, V.parahaemolyticus and Vibrio harveyi), indicating that NaTLR13 could be bounden to bacteria through its functional domain. These results suggested that NaTLR13 might play an important role in the defense of N.albiflora against bacteria or viral infection and the data would provide some information for further understanding the regulatory mechanism of the innate immune system in fish.

Protective Efficacy of Novel Oral Biofilm Vaccines against Photobacterium damselae subsp. damselae Infection in Giant Grouper, Epinephelus lanceolatus

Photobacterium damselae subsp. damselae is a pathogen that mainly infects a variety of fish species. There are many antibiotic-resistant strains of Photobacterium damselae subsp. damselae. In a previously published article, we described the production method for a novel oral biofilm vaccine. In the study reported herein, we confirmed the protective effect of the oral biofilm vaccine against Photobacterium damselae subsp. damselae. Twenty-eight days after vaccination, phagocytosis increased by 256% relative to the control group. The mean albumin–globulin ratios of the vaccine groups were significantly lower than the mean albumin–globulin ratios of the control group. There were no significant intergroup differences in lysozyme activity. Mean IgM titers were significantly higher in the vaccine group than in the control group. There was a significant upregulation of the TLR 3, IL-1β, and IL-8 genes in the spleen 28 days after vaccination. The cumulative mortality of the control fish was 84% after challenging fish with the Photobacterium damselae subsp. damselae, while the cumulative mortality of the oral biofilm vaccine (PBV) group was 32%, which was significantly higher than those of the whole-cell vaccine (PWV) and chitosan particle (CP) groups. There is minimal published research on the prevention and treatment of Photobacterium damselae subsp. damselae infection; therefore, this oral biofilm vaccine may represent a new method to fill this gap.