Evolution and species-specific conservation of toll-like receptors in terrestrial vertebrates

AMPed up immunity: 418 whole genomes reveal intraspecific diversity of koala antimicrobial peptides

Characterising functional diversity is a vital element to understanding a species' immune function, yet many immunogenetic studies in non-model organisms tend to focus on only one or two gene families such as the major histocompatibility complex (MHC) or toll-like receptors (TLR). Another interesting component of the eukaryotic innate immune system is the antimicrobial peptides (AMPs). The two major groups of mammalian AMPs are cathelicidins and defensins, with the former having undergone species-specific expansions in marsupials. Here, we utilised data from 418 koala whole genomes to undertake the first comprehensive analysis of AMP diversity across a mammalian wildlife species' range. Overall, allelic diversity was lower than other immune gene families such as MHC, suggesting that AMPs are more conserved, although balancing selection was observed in PhciDEFB12. Some non-synonymous SNPs in the active peptide are predicted to change AMP function through stop gains, change in structure, and increase in peptide charge. Copy number variants (CNVs) were observed in two defensins and one cathelicidin. Interestingly, the most common CNV was the duplication of PhciCATH5, a cathelicidin with activity against chlamydia, which was more common in the southern part of the species range than the north. AMP copy number is correlated with expression levels, so we hypothesise that there is a selective pressure from chlamydia for duplications in PhciCATH5. Future studies should use phenotypic metadata to assess the functional impacts of this gene duplication.

Positive Selection of TLR2 and MyD88 Genes Provides Insights Into the Molecular Basis of Immunological Adaptation in Amphibians

The transition from water to land of amphibians is evolutionarily significant in the history of vertebrates, and immunological adaptation is an important challenge for amphibians to respond to the dramatic changes of the environmental pathogens during their origin and diversification. Toll-like receptors (TLRs) are important pattern recognition receptors for the innate immune response and TLRs signaling pathway play essential roles in the immune responses to pathogens and inflammatory reaction. However, the evolutionary patterns and molecular mechanisms underlying their adaptation in amphibians are poorly documented to date. Here, we determined the coding regions, expression patterns of TLR2 and Myeloid differentiation factor 88 (MyD88) in the large treefrog (Zhangixalus dennysi), and explored the evolutionary patterns of these two genes in amphibians. Quantitative Real-time PCR analyses showed that the TLR2 and MyD88 mRNA were expressed in all the organs/tissues examined, both with the highest levels in the heart and the lowest levels in the body fat for TLR2 and lung for MyD88. The highly conservation and functional significance of these two genes in amphibians were supported based on the sequence characteristics and evolutionary analyses. Significantly positive selection was found to be acting on TLR2 and MyD88 in amphibians based on different site models. Strong signal of positive selection among different amphibian lineages for these two genes was also detected and a series of positively selected sites were identified based on the branch-site analysis. Our results suggest that amphibians have adapted to different pathogenic microorganisms during their transition from the aquatic to terrestrial environment and diversification into various habitats. The present study will provide new insights into the evolutionary process and molecular basis underlying the immunological adaptation in vertebrates.

Immunohistochemical Characterization of Langerhans Cells in the Skin of Three Amphibian Species

The amphibian taxon includes three orders that present different morphological characteristics: Anura, Caudata, and Apoda. Their skin has a crucial role: it acts as an immune organ constituting a physical, chemical, immunological, and microbiological barrier to pathogen insult and conducts essential physiological processes. Amphibians have developed specialized features to protect the vulnerable skin barrier, including a glandular network beneath the skin surface that can produce antimicrobial and toxic substances, thus contributing to the defense against pathogens and predators. This study aims to characterize Langerhans cells in the skin of Lithobates catesbeianus (order: Anura; Shaw, 1802), Amphiuma means (order: Caudata; Garden, 1821), and Typhlonectes natans (order: Apoda; Fischer, 1880) with the following antibodies: Langerin/CD207 (c-type lectin), Major Histocompatibility Complex (MHC)II, and Toll-like receptor (TLR)2 (expressed by different types of DCs). Our results showed Langerhans cells positive for Langerin CD/207 in the epidermis of the three species; moreover, some antigen-presenting cells (APCs) in the connective tissue expressed TLR2 and MHCII. The distribution of the Langerhans cells is very similar in the three amphibians examined, despite their different habitats. A greater knowledge of the amphibian immune system could be useful to better understand the phylogeny of vertebrates and to safeguard amphibians from population declines. Furthermore, the similarities between amphibians' and human skin concerning immunological features may be useful in both biology and translational medicine.

Diversity of selected toll-like receptor genes in cheetahs (Acinonyx jubatus) and African leopards (Panthera pardus pardus)

The anthropogenic impact on wildlife is ever increasing. With shrinking habitats, wild populations are being pushed to co-exist in proximity to humans leading to an increased threat of infectious diseases. Therefore, understanding the immune system of a species is key to assess its resilience in a changing environment. The innate immune system (IIS) is the body's first line of defense against pathogens. High variability in IIS genes, like toll-like receptor (TLR) genes, appears to be associated with resistance to infectious diseases. However, few studies have investigated diversity in TLR genes in vulnerable species for conservation. Large predators are threatened globally including leopards and cheetahs, both listed as 'vulnerable' by IUCN. To examine IIS diversity in these sympatric species, we used next-generation-sequencing to compare selected TLR genes in African leopards and cheetahs. Despite differences, both species show some TLR haplotype similarity. Historic cheetahs from all subspecies exhibit greater genetic diversity than modern Southern African cheetahs. The diversity in investigated TLR genes is lower in modern Southern African cheetahs than in African leopards. Compared to historic cheetah data and other subspecies, a more recent population decline might explain the observed genetic impoverishment of TLR genes in modern Southern African cheetahs. However, this may not yet impact the health of this cheetah subspecies.

Invasion by exogenous RNA: cellular defense strategies and implications for RNA inference

Exogenous RNA poses a continuous threat to genome stability and integrity across various organisms. Accumulating evidence reveals complex mechanisms underlying the cellular response to exogenous RNA, including endo-lysosomal degradation, RNA-dependent repression and innate immune clearance. Across a variety of mechanisms, the natural anti-sense RNA-dependent defensive strategy has been utilized both as a powerful gene manipulation tool and gene therapy strategy named RNA-interference (RNAi). To optimize the efficiency of RNAi silencing, a comprehensive understanding of the whole life cycle of exogenous RNA, from cellular entry to its decay, is vital. In this paper, we review recent progress in comprehending the recognition and elimination of foreign RNA by cells, focusing on cellular entrance, intracellular transportation, and immune-inflammatory responses. By leveraging these insights, we highlight the potential implications of these insights for advancing RNA interference efficiency, underscore the need for future studies to elucidate the pathways and fates of various exogenous RNA forms, and provide foundational information for more efficient RNA delivery methods in both genetic manipulation and therapy in different organisms.

Understanding the evolution of immune genes in jawed vertebrates

Driven by co-evolution with pathogens, host immunity continuously adapts to optimize defence against pathogens within a given environment. Recent advances in genetics, genomics and transcriptomics have enabled a more detailed investigation into how immunogenetic variation shapes the diversity of immune responses seen across domestic and wild animal species. However, a deeper understanding of the diverse molecular mechanisms that shape immunity within and among species is still needed to gain insight into-and generate evolutionary hypotheses on-the ultimate drivers of immunological differences. Here, we discuss current advances in our understanding of molecular evolution underpinning jawed vertebrate immunity. First, we introduce the immunome concept, a framework for characterizing genes involved in immune defence from a comparative perspective, then we outline how immune genes of interest can be identified. Second, we focus on how different selection modes are observed acting across groups of immune genes and propose hypotheses to explain these differences. We then provide an overview of the approaches used so far to study the evolutionary heterogeneity of immune genes on macro and microevolutionary scales. Finally, we discuss some of the current evidence as to how specific pathogens affect the evolution of different groups of immune genes. This review results from the collective discussion on the current key challenges in evolutionary immunology conducted at the ESEB 2021 Online Satellite Symposium: Molecular evolution of the vertebrate immune system, from the lab to natural populations.

Molecular Mechanisms Underlying Vertebrate Adaptive Evolution: A Systematic Review

Adaptive evolution is a process in which variation that confers an evolutionary advantage in a specific environmental context arises and is propagated through a population. When investigating this process, researchers have mainly focused on describing advantageous phenotypes or putative advantageous genotypes. A recent increase in molecular data accessibility and technological advances has allowed researchers to go beyond description and to make inferences about the mechanisms underlying adaptive evolution. In this systematic review, we discuss articles from 2016 to 2022 that investigated or reviewed the molecular mechanisms underlying adaptive evolution in vertebrates in response to environmental variation. Regulatory elements within the genome and regulatory proteins involved in either gene expression or cellular pathways have been shown to play key roles in adaptive evolution in response to most of the discussed environmental factors. Gene losses were suggested to be associated with an adaptive response in some contexts. Future adaptive evolution research could benefit from more investigations focused on noncoding regions of the genome, gene regulation mechanisms, and gene losses potentially yielding advantageous phenotypes. Investigating how novel advantageous genotypes are conserved could also contribute to our knowledge of adaptive evolution.

Peptide Sequence of Pili Subunit Protein 49.8 kDa Shigella flexneri as Antigenic Epitope for Shigellosis Vaccine Development

Objectives

This study investigates the amino acid sequence and identifies antigenic epitopes of 49.8 kilodalton (kDa) pili protein Shigella flexneri, which will be used as candidates for the shigellosis vaccine.

Materials and Methods

Our study is a prospectively descriptive laboratory. We used bacterial isolate of S. flexneri pili isolation was performed using a pili cutter and sodium dodecyl-sulfate polyacrylamide gel electrophoresis. The amino acid sequences were analyzed using liquid chromatography dual mass spectrometry (LC-MS/MS) method in the proteomic laboratory. The target epitope antigenicity analysis was tested using Kolaskar and Tongaonkar Antigenicity software. The Bepired Linear Epitope Prediction software is used for epitope mapping. PymOL software was used for the visualization of proteins and molecular docking. Peptides and antibodies were applied to hemagglutination test and immune response was tested using the dot blot method.

Results

LC-MS/MS analysis results from the mascot server showed that the 49.8 kDa pili protein is S. flexneri similar to the flagellin protein of S. flexneri 1235-66 (ID I6H2T2). The results of antigenicity analysis and epitope mapping showed that areas of protein that has the most potential and antigenic epitopes are the regions 98-111 and 263-290 with the amino acid sequences, QSSTGTNSQSDLDS (Q-S) and DTTITKAETKTVTKNQVVDTPVTTDAAK (D-K). The results of the molecular docking interaction test between the peptide and the B-cell receptor have a low binding energy. Peptide Q-S and peptide D-K antigens are hemagglutinin molecules because they can agglutinate erythrocytes. The immune response between peptide antigens and anti-peptide antibodies can react based on color gradations in the dotblot method.

Conclusion

The amino acid sequences Q-S and D-K are potentially antigenic epitopes. These peptides can be used to develop candidates for shigellosis vaccine.

Application and prospect of targeting innate immune sensors in the treatment of autoimmune diseases

Dysregulation of auto-reactive T cells and autoantibody-producing B cells and excessive inflammation are responsible for the occurrence and development of autoimmune diseases. The suppression of autoreactive T cell activation and autoantibody production, as well as inhibition of inflammatory cytokine production have been utilized to ameliorate autoimmune disease symptoms. However, the existing treatment strategies are not sufficient to cure autoimmune diseases since patients can quickly suffer a relapse following the end of treatments. Pattern recognition receptors (PRRs), including Toll-like receptors (TLRs), Nod-like receptors (NLRs), RIG-I like receptors (RLRs), C-type lectin receptors (CLRs) and various nucleic acid sensors, are expressed in both innate and adaptive immune cells and are involved in the development of autoimmune diseases. Here, we have summarized advances of PRRs signaling pathways, association between PRRs and autoimmune diseases, application of inhibitors targeting PRRs and the corresponding signaling molecules relevant to strategies targeting autoimmune diseases. This review emphasizes the roles of different PRRs in activating both innate and adaptive immunity, which can coordinate to trigger autoimmune responses. The review may also prompt the formulation of novel ideas for developing therapeutic strategies against autoimmune diseases by targeting PRRs-related signals.

Immunoglobulin-like receptors and the generation of innate immune memory

Host immunity is classically divided into "innate" and "adaptive." While the former has always been regarded as the first, rapid, and antigen-nonspecific reaction to invading pathogens, the latter represents the more sophisticated and antigen-specific response that has the potential to persist and generate memory. Recent work however has challenged this dogma, where murine studies have successfully demonstrated the ability of innate immune cells (monocytes and macrophages) to acquire antigen-specific memory to allogeneic major histocompatibility complex (MHC) molecules. The immunoreceptors so far identified that mediate innate immune memory are the paired immunoglobulin-like receptors (PIRs) in mice, which are orthologous to human leukocyte immunoglobulin-like receptors (LILRs). These receptor families are mainly expressed by the myelomonocytic cell lineage, suggesting an important role in the innate immune response. In this review, we will discuss the role of immunoglobulin-like receptors in the development of innate immune memory across species.

Comparison of flagellin and an oil-emulsion adjuvant in inactivated Newcastle disease vaccine in stimulation of immunogenic parameters

The present study was designed to investigate the potential application of native (N) and recombinant (truncated modified [tmFliC] and full-length [flFliC]) flagellin proteins along with inactivated Newcastle disease virus (NDV). Fifty six SPF chickens were immunized twice with PBS (control), inactivated NDV (Ag), inactivated NDV/flFliC (AgF), inactivated NDV/tmFliC (AgT), inactivated NDV/N (AgN), commercial vaccine containing Montanide (Vac) and Vac/N (VacN), with a two-week interval. Blood was collected weekly and spleens were harvested after chickens were sacrificed. Interleukin-6 (IL-6) and tumor necrotic factor-α (TNF-α) gene expression in peripheral blood mononuclear cells were analyzed by Real-Time PCR. Antibody response was assessed by haemagglutination inhibition (HI). Cellular activity was quantified by MTT assay. Results showed that the most IL-6 and TNF-α gene expression was observed in AgF group (P < 0.01). The lowest gene expression among vaccinated groups was observed in Ag group for IL-6 and Ag and Vac group for TNF-α. The highest HI titer was observed in Vac, VacN, AgF and AgT groups. The AgF group showed the highest cellular activity (P < 0.01). In conclusion, flagellin-adjuvanted groups showed a pro-inflammatory effect and acted similarly to or better than the Vac group. Hence, flagellin can be proposed as a potential adjuvant for ND vaccine.

Variation in selection constraints on teleost TLRs with emphasis on their repertoire in the Walking catfish, Clarias batrachus

The high degree of conservation of toll-like receptors (TLRs), and yet their subtle variations for better adaptation of species in the host–pathogen arms race make them worthy candidates for understanding evolution. We have attempted to track the trend of TLR evolution in the most diverse vertebrate group—teleosts, where Clarias batrachus was given emphasis, considering its traits for terrestrial adaptation. Eleven C. batrachus TLRs (TLR1, 2, 3, 5, 7, 8 9, 13, 22, 25, 26) were identified in this study which clustered in proximity to its Siluriformes relative orthologues in the phylogenetic analysis of 228 TLRs from 25 teleosts. Ten TLRs (TLR1, 2, 3, 5, 7, 8 9, 13, 21, 22) with at least 15 member orthologues for each alignment were processed for selection pressure and coevolutionary analysis. TLR1, 7, 8 and 9 were found to be under positive selection in the alignment-wide test. TLR1 also showed maximum episodic diversification in its clades while the teleost group Eupercaria showed the maximum divergence in their TLR repertoire. Episodic diversification was evident in C. batrachus TLR1 and 7 alignments. These results present a strong evidence of a divergent TLR repertoire in teleosts which may be contributing towards species-specific variation in TLR functions.

Effect of flagellin on inhibition of infectious mechanisms by activating opsonization and salmonella flagellum disruption

Some serovars of salmonella cause huge global diseases such as enteric fever and invasive non typhoidal Salmonella disease. Flagellin as a key antigenic component of salmonella, can induce humoral and cellular immunity responses. In this research, we performed an opsonophagocytic killing assay (OPKA) as an important mechanism of the host-defense system, for salmonella to study the activity of anti-sera of native FliC, truncated modified recombinant FliC (tmFliC) and full length recombinant FliC proteins (flFliC). Also, the potency of antibodies for inhibiting bacterial movement was evaluated by traditional and newly-designed motility inhibition assay methods. Results showed both recombinant FliC anti-sera and native FliC (nFliC) anti-serum had the ability to opsonize Salmonella typhimurim, which led to bacterial clearance by mice macrophages. Also, inhibition of bacterial motility was observed for all anti-sera. Anti-nFliC and anti-flFliC sera showed higher effects on Salmonella typhimurim motility than that of tmFliC. In traditional method, about 88%, 86% and 80% inhibition were observed by using 5% nFliC, anti-flFliC and anti-tmFliC sera, respectively. In the newly-designed method using SIM (Sulfide indole motility) medium, results confirmed the traditional method for motility inhibition. Our findings suggest that salmonella fliC as a protective antigen may disrupt the flagellum apparatus activity.

Molecular evolution in immune genes across the avian tree of life

All organisms encounter pathogens, and birds are especially susceptible to infection by malaria parasites and other haemosporidians. It is important to understand how immune genes, primarily innate immune genes which are the first line of host defense, have evolved across birds, a highly diverse group of tetrapods. Here, we find that innate immune genes are highly conserved across the avian tree of life and that although most show evidence of positive or diversifying selection within specific lineages or clades, the number of sites is often proportionally low in this broader context of putative constraint. Rather, the evidence shows a much higher level of negative or purifying selection in these innate immune genes - rather than adaptive immune genes - which is consistent with birds' long coevolutionary history with pathogens and the need to maintain a rapid response to infection. We further explored avian responses to haemosporidians by comparing differential gene expression in wild birds (1) uninfected with haemosporidians, (2) infected with Plasmodium, and (3) infected with Haemoproteus (Parahaemoproteus). We found patterns of significant differential expression with some genes unique to infection with each genus and a few shared between "treatment" groups, but none that overlapped with the genes included in the phylogenetic study.

Adjuvants: What a Difference 15 Years Makes!

Vaccination is a critical tool in modern animal production and key to maintaining animal health. Adjuvants affect the immune response by increasing the rate, quantity, or quality of the protective response generated by the target antigens. Although adjuvant technology dates back to the nineteenth century, there was relatively little improvement in adjuvant technology before the late twentieth century. With the discovery of molecular pathways that regulate the timing, quantity, and quality of the immune response, new technologies are focused on bringing safer, more effective, and inexpensive adjuvants to commercial use.

Immunostimulatory effects of truncated and full-length flagellin recombinant proteins

Problems regarding purification efficacy in recombinant technologies is due to the protein structure. Experimental manipulation of genes and the subsequent proteins may overcome this issue. In order to improve production efficacy and maintain immunestimulatory effect of flagellin, the Toll-like Receptor 5 (TLR5) ligand and a potent adjuvant, we performed a bioinformatic study to find the best model for FliC manipulation. Truncated modified FliC (tmFliC) and full length FliC (flFliC) genes were cloned and expressed in pET-21a vector and protein purification was carried out using an improved His-Tag method. Polyclonal antibodies were generated against flFliC and tmFliC in New Zealand white rabbits. IgG response to the recombinant proteins was determined by ELISA. Cross-reactivity assay was performed by ELISA for all proteins and bacteria. Immunogenicity of tmFliC and flFliC was evaluated in chicken cells, and expression level of tumor necrotic factor-α (TNF-α) and interleukin-6 (IL-6) were relatively analyzed by Real-Time-PCR. Results showed high purification efficacy for tmFliC. Antibody titer of tmFliC was significantly higher than that of flFliC. In addition, the cross-reactivity assay for both proteins and Salmonella was positive which indicates similar epitopic regions. Stimulation of both FliCs significantly increased TNF-α and IL-6 expression in peripheral blood mononuclear cells (PBMCs) and splenocytes, with higher effect observed with flFliC. IL-8 protein level increased after 6 and 24 h stimulation with different concentrations of tmFliC and flFliC. These results suggest that the aimed gene modification in fliC gene produces a bioactive immunostimulant type of flagellin which upregulates TLR5 downstream genes as well as in flFliC.