Characterization and expression profiling of NOD-like receptor C3 (NLRC3) in mucosal tissues of turbot (Scophthalmus maximus L.) following bacterial challenge

Single-cell transcriptome landscape of the kidney reveals potential innate immune regulation mechanisms in hybrid yellow catfish after Aeromonas hydrophila infection

Aeromonas hydrophila, the pathogen that is the causative agent of motile Aeromonas septicemia (MAS) disease, commonly attacks freshwater fishes, including yellow catfish (Pelteobagrus fulvidraco). Although the kidney is one of the most important organs involved in immunity in fish, its role in disease progression has not been fully elucidated. Understanding the cellular composition and innate immune regulation mechanisms of the kidney of yellow catfish is important for the treatment of MAS. In this study, single-cell RNA sequencing (scRNA-seq) was performed on the kidney of hybrid yellow catfish (Pelteobagrus fulvidraco ♀ × Pelteobagrus vachelli ♂) after A. hydrophila infection. Nine types of kidney cells were identified using marker genes, and a transcription module of marker genes in the main immune cells of hybrid yellow catfish kidney tissue was constructed using in-situ hybridization. In addition, the single-cell transcriptome data showed that the differentially expressed genes of macrophages were primarily enriched in the Toll-like receptor and Nod-like receptor signaling pathways. The expression levels of genes involved in these pathways were upregulated in macrophages following A. hydrophila infection. Transmission electron microscopy and TUNEL analysis revealed the cellular characteristics of macrophages before and after A. hydrophila infection. These data provide empirical support for in-depth research on the role of the kidney in the innate immune response of hybrid yellow catfish.

In vitro analysis of the expression of inflammasome, antiviral, and immune genes in an Oreochromis niloticus liver cell line following stimulation with bacterial ligands and infection with tilapia lake virus

The inflammasome is a multimeric protein complex that plays a vital role in the defence against pathogens and is therefore considered an essential component of the innate immune system. In this study, the expression patterns of inflammasome genes (NLRC3, ASC, and CAS-1), antiviral genes (IFNγ and MX), and immune genes (IL-1β and IL-18) were analysed in Oreochromis niloticus liver (ONIL) cells following stimulation with the bacterial ligands peptidoglycan (PGN) and lipopolysaccharide (LPS) and infection with TiLV. The cells were stimulated with PGN and LPS at concentrations of 10, 25, and 50 µg/ml. For viral infection, 106 TCID50 of TiLV per ml was used. After LPS stimulation, all seven genes were found to be expressed at specific time points at each of the three doses tested. However, at even higher doses of LPS, NLRC3 levels decreased. Following TiLV infection, all of the genes showed significant upregulation, especially at early time points. However, the gene expression pattern was found to be unique in PGN-treated cells. For instance, NLRC3 and ASC did not show any response to PGN stimulation, and the expression of IFNγ was downregulated at 25 and 50 µg of PGN per ml. CAS-1 and IL-18 expression was downregulated at 25 µg of PGN per ml. At a higher dose (50 µg/ml), IL-1β showed downregulation. Overall, our results indicate that these genes are involved in the immune response to viral and bacterial infection and that the degree of response is ligand- and dose-dependent.

Regulation of NF-κB signaling by NLRC (NLRC3-like) gene in the common carp (Cyprinus carpio)

Among teleost NLRs, NLR-C subfamily is a large group of proteins that were teleost-specific and evolution analysis showed that NLR-Cs are most likely to evolve from NLRC3 gene (thus also called as NLRC3Ls). Presently, although there have been rich studies investigating teleost NLRC3 and NLRC3L, the data on the regulatory mechanism was limited. In this study, immune regulation of inflammatory signaling pathway mediated by common carp NLRC3L gene (CcNLRC) has been investigated. Confocal microscopy analysis showed that CcNLRC was located in cytoplasm, and in HEK293T cells, dual-luciferase reporter assay showed the regulation of NF-κB signaling by CcNLRC, in which CcNLRC could alter/decrease RIPK2-induced activation of NF-κB. These results indicated that CcNLRC may function as a negative NLR in the regulation of inflammatory response in common carp. Our data will allow to gain more insights into the molecular mechanism of teleost specific NLR (NLRC3L).

A review of soluble factors and receptors involved in fish skin immunity: The tip of the iceberg

The immune system of fish possesses soluble factors, receptors, pathways and cells very similar to those of the other vertebrates' immune system. Throughout evolutionary history, the exocrine secretions of organisms have accumulated a large reservoir of soluble factors that serve to protect organisms from microbial pathogens that could disrupt mucosal barrier homeostasis. In parallel, a diverse set of recognition molecules have been discovered that alert the organism to the presence of pathogens. The known functions of both the soluble factors and receptors mentioned above encompass critical aspects of host defense, such as pathogen binding and neutralization, opsonization, or modulation of inflammation if present. The molecules and receptors cooperate and are able to initiate the most appropriate immune response in an attempt to eliminate pathogens before host infection can begin. Furthermore, these recognition molecules, working in coordination with soluble defence factors, collaboratively erect a robust and perfectly coordinated defence system with complementary specificity, activity and tissue distribution. This intricate network constitutes an immensely effective defence mechanism for fish. In this context, the present review focuses on some of the main soluble factors and recognition molecules studied in the last decade in the skin mucosa of teleost fish. However, knowledge of these molecules is still very limited in all teleosts. Therefore, further studies are suggested throughout the review that would help to better understand the functions in which the proteins studied are involved.

The evolution of NLRC3 subfamily genes in Sebastidae teleost fishes

BACKGROUND

With more than 36,000 valid fish species, teleost fishes constitute the most species-rich vertebrate clade and exhibit extensive genetic and phenotypic variation, including diverse immune defense strategies. NLRC3 subfamily genes, which are specific to fishes, play vital roles in the immune system of teleosts. The evolution of teleosts has been impacted by several whole-genome duplication (WGD) events, which might be a key reason for the expansions of the NLRC3 subfamily, but detailed knowledge of NLRC3 subfamily evolution in the family Sebastidae is still limited.

RESULTS

Phylogenetic inference of NLRC3 subfamily protein sequences were conducted to evaluate the orthology of NLRC3 subfamily genes in black rockfish (Sebastes schlegilii), 13 other fish species from the families Sebastidae, Serranidae, Gasterosteidae and Cyclopteridae, and three species of high vertebrates (bird, reptile and amphibian). WGD analyses were used to estimate expansions and contractions of the NLRC3 subfamily, and patterns of expression of NLRC3 subfamily genes in black rockfish following bacterial infections were used to investigate the functional roles of these genes in the traditional and mucosal immune system of the Sebastidae. Different patterns of gene expansions and contractions were observed in 17 fish and other species examined, and one and two whole-genome duplication events were observed in two members of family Sebastidae (black rockfish and honeycomb rockfish, Sebastes umbrosus), respectively. Subsequently, 179 copy numbers of NLRC3 genes were found in black rockfish and 166 in honeycomb rockfish. Phylogenetic analyses corroborated the conservation and evolution of NLRC3 orthologues between Sebastidae and other fish species. Finally, differential expression analyses provided evidence of the immune roles of NLRC3 genes in black rockfish during bacterial infections and gene ontology analysis also indicated other functional roles.

CONCLUSIONS

We hypothesize that NLRC3 genes have evolved a variety of different functions, in addition to their role in the immune response, as a result of whole genome duplication events during teleost diversification. Importantly, this study had underscored the importance of sampling across taxonomic groups, to better understand the evolutionary patterns of the innate immunity system on which complex immunological novelties arose. Moreover, the results in this study could extend current knowledge of the plasticity of the immune system.

Genome-wide identification, phylogenetic relationships and expression patterns of the NOD-like receptor (NLR) gene family in flounder (Paralichthys olivaceus)

NOD-like receptors (NLRs) are one of the pattern recognition receptors which have been widely known for identifying pathogens and regulating innate immunity in mammals, but the functions of the NLR gene family in teleost fish remain poorly understood. In this study, we conducted a comprehensive identification and analysis of the flounder (Paralichthys olivaceus) NLR gene family, including bioinformatics information, evolutionary relationships, gene structures, conserved motifs, domain composition, expression patterns and protein-protein interaction (PPI). We identified 22 NLRs in flounder (flNLRs) which were clustered into three subfamilies according to their domain organizations and phylogenetic features, i.e., NLR-A (6 members) resembling mammalian NODs, NLR-B (1 member) resembling mammalian NLRPs, and NLR-C (15 members) unique to teleost fish. All flNLRs shared a conserved NACHT domain including an N-terminal nucleotide-binding domain, a middle helical domain 1, and a winged helix domain. Gene structure analysis displayed that flNLRs were significantly different, with exon numbers from 1 to 52. Conserved domain analysis showed that the N-terminus of flNLRs possessed different characteristics of the domains including CARD domain, PYRIN domain, RING domain, and fish-specific FISNA domain, and the C-terminus of seven NLR-C members contained an extra B30.2 domain, named NLRC-B30.2 group. Notably, flNLRs were expressed in all nine tested tissues, showing higher expressions in the systemic and mucosal immune tissues (e.g., kidney, spleen, hindgut, gills, skin, liver) in healthy flounder, and significant responses to intraperitoneal injection and immersion immunization of inactivated Vibrio anguillarum in mucosal tissues, especially the NLR-C members. In addition, PPI analysis demonstrated that some flNLRs of NLR-A and NLR-C shared the same interacting proteins such as RIPK2, TRAF6, MAVS, CASP, ASC, and ATG5, suggesting they might play crucial roles in host defense, antiviral innate immunity, inflammation, apoptosis and autophagy. This study for the first time characterized the NLR gene family of flounder at the genome-wide level, and the results provided a better understanding of the evolution of the NLR gene family and their immune functions in innate immunity in fish.

New insights into β-glucan-enhanced immunity in largemouth bass Micropterus salmoides by transcriptome and intestinal microbial composition

β-glucan is widely used in aquaculture due to its immunostimulatory effects, but the specific effect and potential regulatory mechanism on largemouth bass (Micropterus salmoides) are still unclear. Here, we evaluated the effects of β-glucan on growth, resistance to Aeromonas schubertii, intestinal health, and transcriptome of largemouth bass to reveal the potential regulators, metabolic pathways, and altered differential microbiota. Four experimental diets were designed with β-glucan supplementation levels of 0 (control), 100 (LA-100), 200 (MA-200), and 300 (HA-300) mg kg^-1, and each diet was fed to largemouth bass (79.30 ± 0.50 g) in triplicate for 70 days, followed by a 3-day challenge experiment. Results showed that different β-glucan supplementations had no significant effects on growth performance and whole-body composition. Fish fed a diet with 300 mg kg^-1 β-glucan significantly increased the activity of lysozyme than those fed diets with 0 and 100 mg kg^-1 β-glucan. In addition, the survival rate of largemouth bass in β-glucan supplementation groups was significantly higher than the control group at 12- and 24-h challenge by Aeromonas schubertii. Transcriptome analysis showed that a total of 1,245 genes were differentially expressed [|log₂(fold change)| ≥1, q-value ≤0.05], including 109 immune-related differentially expressed genes (DEGs). Further analysis revealed that significantly upregulated and downregulated DEGs associated with immunity were mapped into 12 and 24 pathways, respectively. Results of intestinal microflora indicated that fish fed a diet with 300 mg kg^-1 β-glucan had higher bacterial richness and diversity as evaluated by Sobs, Chao, Ace, and Simpson indices, but no significant differences were found in the comparison groups. Furthermore, 300 mg kg^-1 β-glucan significantly increased the relative abundance of Mycoplasma and decreased Proteobacteria (mainly Escherichia-Shigella and Escherichia coli) and Bacillus anthracis in largemouth bass intestinal microflora. The findings of this study provided new insights that will be valuable in future studies to elucidate the mechanism of immunity enhancement by β-glucan.

NLRC3 deficiency promotes cutaneous wound healing due to the inhibition of p53 signaling

Cutaneous wound healing is a complicated process that is characterized by an initial inflammatory phase followed by a proliferative phase. NLRC3 plays important roles in innate immunity, inflammatory regulation and tumor cell growth. However, the function of NLRC3 in wound healing remains unclear. Here, we investigated the function of NLRC3 in acute cutaneous wound healing using Nlrc3 gene knockout (Nlrc3^-/-) mice. Our results demonstrated that skin wound repair in Nlrc3^-/- mice was significantly accelerated compared with that in wild-type (WT) mice. NLRC3 deficiency promoted the inflammatory and proliferative phases in wounds enhanced the inflammatory response and increased re-epithelialization and granulation tissue formation, and these phenotypes were primarily ascribed to regulatory effects on p53 signaling. Mechanistically, we uncovered novel crosstalk between NLRC3 and p53 signaling and revealed that NLRC3 could mediate the ubiquitination and degradation of p53 in an Hsp90-dependent manner. In conclusion, our study suggests that NLRC3 is a critical negative regulator of the inflammatory response and cell proliferation during wound healing and that blocking NLRC3 may represent a potential approach for accelerating wound healing.

NLRC3 attenuates antiviral immunity and activates inflammasome responses in primary grouper brain cells following nervous necrosis virus infection

NLRC3 is identified as a unique regulatory NLR involved in the modulation of cellular processes and inflammatory responses. In this study, a novel Nod like receptor C3 (NLRC3) was functionally characterized from seven band grouper in the context of nervous necrosis virus infection. The grouper NLRC3 is highly conserved and homologous with other vertebrate proteins with a NACHT domain and a C-terminal leucine-rich repeat (LRR) domain and an N-terminal CARD domain. Quantitative gene expression analysis revealed the highest mRNA levels of NLRC3 were in the brain and gill followed by the spleen and kidney following NNV infection. Overexpression of NLRC3 augmented the NNV replication kinetics in primary grouper brain cells. NLRC3 attenuated the interferon responses in the cells following NNV infection by impacting the TRAF6/NF-κB activity and exhibited reduced IFN sensitivity, ISRE promoter activity, and IFN pathway gene expression. In contrast, NLRC3 expression positively regulated the inflammasome response and pro-inflammatory gene expression during NNV infection. NLRC3 negatively regulates the PI3K-mTOR axis and activated the cellular autophagic response. Delineating the complexity of NLRC3 regulation of immune response in the primary grouper brain cells following NNV infection suggests that the protein acts as a virally manipulated host factor that negatively regulated the antiviral immune response to augment the NNV replication.

Identification of mRNA-miRNA-lncRNA regulatory network associated with the immune response to Aeromonas salmonicides infection in the black rockfish (Sebastes schlegelii)

In aquaculture, Aeromonas salmonicides (A. salmonicida) is a main fish pathogen because of its nearly worldwide distribution, and broad host range. Recently, an increasing number of evidences have uncovered the roles of mRNA-miRNA-lncRNA network in fish diseases. In current study, RNA-seq was conducted in the black rockfish spleen following A. salmonicida infection at 0 h (Sp0 or control) and three different post-infection time-points (2 h: Sp2, 12 h: Sp12 and 24 h: Sp24, respectively) to comprehensively identify differentially expressed (DE) mRNAs, miRNAs and lncRNAs. Enrichment analysis and protein-protein interaction (PPI) analysis of DE mRNAs were performed. Then, expression and correlation analysis for mRNAs and their upstream miRNAs and lncRNAs were conducted. Finally, a total of 1364 mRNAs, 17 miRNAs and 1584 lncRNAs exhibited significantly differential expressions during bacterial infection in the black rockfish spleen. Functional enrichment analysis suggested that they were significantly enriched in several immune-related pathways, including Amino sugar and nucleotide sugar metabolism, Cell adhesion molecules (CAMs), Neuroactive ligand-receptor interaction, Nicotinate and nicotinamide metabolism, Pentose and glucuronate interconversions, Phagosome, Proteasome, etc. Subsequently, 1091 lncRNA-miRNA-mRNA pathways (323 in Sp2, 609 in Sp12 and 207 in Sp24) were constructed including 400 lncRNAs, 69 miRNAs, and 70 mRNAs. Meanwhile, NLRC3/novel-264/LNC_00116154 pathway demonstrated important immune modulating function in the black rockfish against A. salmonicida infection. Finally, the novel mRNA-miRNA-lncRNA sub-networks were established, among which all mRNAs and ncRNAs possessed significant predictive values for further studies for immune responses in the black rockfish.

A genome-wide survey of NOD-like receptors in Chinese tongue sole (Cynoglossus semilaevis): Identification, characterization and expression analysis in response to bacterial infection

As intracellular pathogen recognition receptors (PRRs), nucleotide-binding domain, leucine-rich repeat containing receptors (NLRs, NOD-like receptors) are involved in innate immune responses in vertebrates. However, there is no systemic study on NLRs in Chinese tongue sole (Cynoglossus semilaevis), a popular maricultured fish in China. In the present study, a genome-wide survey of NLRs was performed in C. semilaevis, with the identification of 29 NLRs, including five genes from the NLR-A subfamily (referred to as CsNOD1-5), two genes from the NLR-B subfamily, 18 genes from the NLR-C subfamily (referred to as CsNLR-C1 to 18) and four other NLR genes. Phylogenetic analysis implied that CsNOD1-5 contained conserved functional domains and had orthologous relationships with human NOD1-5. Moreover, CsNLR-C genes all possessed the FISHNA domain, which is a fish-specific NACHT subdomain. Expression analysis showed that CsNOD1-5 and CsNLR-C1/2 were ubiquitously expressed in various normal tissues. Bacterial infection with Vibro harveyi revealed distinct expression patterns of all the tested CsNLRs in gill, intestine, trunk kidney, liver and spleen. In particular, CsNOD1-4 and CsNLR-C2 were significantly upregulated in gills at 48 h post bacterial infection. In addition, CsNOD3 and CsNOD4 were significantly elevated in infectious intestine, trunk kidney, liver and spleen, revealing that their expressions were more sensitive to bacterial infection than other CsNLRs. Together with the computational protein-protein interaction network of CsNLRs, it was suggested that individual NLR genes had different roles in the innate immune cascades of C. semilaevi against bacterial infection. This study provides valuable information for further studies on CsNLR immune function.

Recurrent expansions of B30.2-associated immune receptor families in fish

B30.2 domains, also known as PRY/SPRY, are key components of specific subsets of two large families of proteins involved in innate immunity: the tripartite motif proteins (TRIMs) and the Nod-like receptors (NLRs). TRIM proteins are important, often inducible factors of antiviral innate immunity, targeting multiple steps of viral cycles through a variety of mechanisms. NLRs prime and regulate systemic innate defenses, especially against bacteria, and control inflammation. Large TRIM and NLR subsets characterized by the presence of a B30.2 domain have been reported from a few fish species including zebrafish and seem to be strongly prone to gene duplication/expansion. Here, we performed a large-scale survey of these receptors across about 150 fish genomes, focusing on ray-finned fishes. We assessed the number and genomic distribution of domains and domain combinations associated with TRIMs, NLRs, and other genes containing B30.2 domains and looked for gene expansion patterns across fish groups. We then used a model to test the impact of taxonomy, genome size, and environmental variables on the copy numbers of these genes. Our findings reveal novel domain structures, clade-specific gains and losses. They also assist with the timing of the gene expansions, reveal patterns associated with the MHC, and lay the groundwork for further studies delving deeper into the forces that drive the copy number variation of immune genes on a species level.

Molecular cloning and immune characterization of CIITA in artificially challenged Chinese tongue sole (Cynoglossus semilaevis) with Vibrio harveyi

In mammals, Class II, major histocompatibility complex (MHC II) transactivator (CIITA) recognizes microbial pathogens and triggers immune responses. In Chinese tongue sole Cynoglossus semilaevis, Cs-CIITA was prevalently expressed in various tissues. Cs-CIITA, Cs-MHC IIA and Cs-MHC IIB were expressed significantly higher in skin in susceptible families infected with Vibrio harveyi, while higher expression of Cs-CIITA and Cs-MHC IIB was examined in liver in resistant families. In addition, the three genes were up-regulated in gill, skin, intestine, liver, spleen and kidney at 48 h or 72 h after V. harveyi infection. Furthermore, the three genes were co-expressed in the epithelial mucous cells of gill, skin, and intestine. Knockdown of Cs-CIITA regulates the expression of other inflammation-related genes, including CD40, IL-1β, IL-8, RelB, NFκB, and Myd88. These results suggest that CIITA functions in the inflammatory responses of C. semilaevis against V. harveyi, via MHC II transcriptional regulation.

Carvacrol, Thymol, and Garlic Essential Oil Promote Skin Innate Immunity in Gilthead Seabream (Sparus aurata) Through the Multifactorial Modulation of the Secretory Pathway and Enhancement of Mucus Protective Capacity

One of the main targets for the use of phytogenics in aquafeeds is the mucosal tissues as they constitute a physical and biochemical shield against environmental and pathogenic threats, comprising elements from both the innate and acquired immunity. In the present study, the modulation of the skin transcriptional immune response, the bacterial growth capacity in skin mucus, and the overall health condition of gilthead seabream (Sparus aurata) juveniles fed a dietary supplementation of garlic essential oil, carvacrol, and thymol were assessed. The enrichment analysis of the skin transcriptional profile of fish fed the phytogenic-supplemented diet revealed the regulation of genes associated to cellular components involved in the secretory pathway, suggesting the stimulation, and recruitment of phagocytic cells. Genes recognized by their involvement in non-specific immune response were also identified in the analysis. The promotion of the secretion of non-specific immune molecules into the skin mucus was proposed to be involved in the in vitro decreased growth capacity of pathogenic bacteria in the mucus of fish fed the phytogenic-supplemented diet. Although the mucus antioxidant capacity was not affected by the phytogenics supplementation, the regulation of genes coding for oxidative stress enzymes suggested the reduction of the skin oxidative stress. Additionally, the decreased levels of cortisol in mucus indicated a reduction in the fish allostatic load due to the properties of the tested additive. Altogether, the dietary garlic, carvacrol, and thymol appear to promote the gilthead seabream skin innate immunity and the mucus protective capacity, decreasing its susceptibility to be colonized by pathogenic bacteria.

Genome-wide identification of NOD-like receptors and their expression profiling in mucosal tissues of turbot (Scophthalmus maximus L.) upon bacteria challenge

The innate immune system plays an important role in host defense against pathogenic infections. In the innate immune system, several families of innate pattern recognition receptors, including Toll-like receptors, RIG-I-like receptors, NOD-like receptors (NLRs), and DNA receptors (cytosolic sensors for DNA), are known to play vital roles in detecting and responding to various pathogens. In this study, we identified 29 NLRs in turbot including 4 NLRs from subfamily A: NOD1, NOD2, CIITA, NLRC5, 1 NLR from subfamily B: NLRB1, 21 NLRs from subfamily C: NLR-C3.1∼NLRC3.21, 1 from NLRX subfamily, and two that do not fall within these subfamilies: APAF1, NWD1. Phylogenetic analysis showed that these NLR genes were clearly divided into five subfamilies. Protein-protein interaction network analysis showed that some of these NLR genes shared same interacting genes and might participate in signal transductions associated with immunity. The evolutionary pressure selection analysis showed that the Ka/Ks ratios for all detected NLR genes were much less than one, implying more synonymous changes than non-synonymous changes. In addition, tissue expression analysis showed that the relative higher expression levels were observed in gill, skin and intestine. Meanwhile, NLR genes expression after bacterial infection results showed that most NLR genes participated in the process of defense of V. anguillarum and A. salmonicida infections in mucosal tissues. Taken together, identification and expression profiling analysis of NLR genes can provide valuable information for further functional characterization of these genes in turbot.

Investigating mechanisms underlying genetic resistance to Salmon Rickettsial Syndrome in Atlantic salmon using RNA sequencing

Background

Salmon Rickettsial Syndrome (SRS), caused by Piscirickettsia salmonis, is one of the primary causes of morbidity and mortality in Atlantic salmon aquaculture, particularly in Chile. Host resistance is a heritable trait, and functional genomic studies have highlighted genes and pathways important in the response of salmon to the bacteria. However, the functional mechanisms underpinning genetic resistance are not yet well understood. In the current study, a large population of salmon pre-smolts were challenged with P. salmonis, with mortality levels recorded and samples taken for genotyping. In parallel, head kidney and liver samples were taken from animals of the same population with high and low genomic breeding values for resistance, and used for RNA-Sequencing to compare their transcriptome profile both pre and post infection.

Results

A significant and moderate heritability (h² = 0.43) was shown for the trait of binary survival. Genome-wide association analyses using 38 K imputed SNP genotypes across 2265 animals highlighted that resistance is a polygenic trait. Several thousand genes were identified as differentially expressed between controls and infected samples, and enriched pathways related to the host immune response were highlighted. In addition, several networks with significant correlation with SRS resistance breeding values were identified, suggesting their involvement in mediating genetic resistance. These included apoptosis, cytoskeletal organisation, and the inflammasome.

Conclusions

While resistance to SRS is a polygenic trait, this study has highlighted several relevant networks and genes that are likely to play a role in mediating genetic resistance. These genes may be future targets for functional studies, including genome editing, to further elucidate their role underpinning genetic variation in host resistance.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07443-2.

Characterization and expression analysis of mitochondrial localization molecule: NOD-like receptor X1 (Nlrx1) in mucosal tissues of turbot (Scophthalmus maximus) following bacterial challenge

The NOD-like receptor X1 (NLRX1) is a member of highly conserved nucleotide-binding domain (NBD)- and leucine-rich-repeat (LRR)-containing family (known as NLR), that localizes to the mitochondrial outer membrane and regulate the innate immunity by interacting with mitochondrial antiviral-signaling protein (MAVS). As one of cytoplasmic PRRs, NLRX1 plays key roles for pathogen recognition, autophagy and regulating of subsequent immune signaling pathways. In this study, we identified the nlrx1 in turbot as well as its expression profiles in mucosal surfaces following bacterial infection. In our results, the full-length nlrx1 transcript consists of an open reading frame (ORF) of 4,886 bp encoding the putative peptide of 966 amino acids. The phylogenetic analysis revealed the SmNlrx1 showed the closest relationship to Cynoglossus semilaevis. In addition, the Nlrx1 mRNA expression could be detected in all the examined tissues, with the most abundant expression level in head kidney, and the lowest expression level in liver. Moreover, Nlrx1 showed similar expression patterns following Vibrio anguillarum and Streptococcus iniae infection, that were both significantly up-regulated following challenge, especially post S. iniae challenge. Finally, fluorescence microscopy unveiled that the SmNlrx1 localized to mitochondria in HEK293T by N-terminal mitochondrial targeting sequence. Characterization of Nlrx1 might have an important implication in bioenergetic adaptation during metabolic stress, oncogenic transformation and innate immunity and will probably contribute to the development of novel intervention strategies for farming turbot.

The rice LRR-like1 protein YELLOW AND PREMATURE DWARF 1 is involved in leaf senescence induced by high light

Senescence in plants is induced by endogenous physiological changes and exogenous stresses. In this study, we isolated two alleles of a novel rice (Oryza sativa) mutant, yellow and premature dwarf 1 (ypd1). The ypd1 mutants exhibited a yellow and dwarf phenotype from germination, and premature senescence starting at tillering. Moreover, the ypd1 mutants were sensitive to high light, which accelerated cell death and senescence. Consistent with their yellow phenotype, the ypd1 mutants had abnormal chloroplasts and lower levels of photosynthetic pigments. TUNEL assays together with histochemical staining demonstrated that ypd1 mutants showed cell death and that they accumulated reactive oxygen species. The ypd1 mutants also showed increased expression of genes associated with senescence. Map-based cloning revealed a G→A substitution in exon 6 (ypd1-1) and exon 13 (ypd1-2) of LOC_Os06g13050 that affected splicing and caused premature termination of the encoded protein. YPD1 was found to be preferentially expressed in the leaf and it encodes a LRR-like1 protein. Complementation, overexpression, and targeted deletion confirmed that the mutations in YPD1 caused the ypd1 phenotype. YPD1 was localized on the chloroplast membrane. Our results thus demonstrate that the novel rice LRR-like1 protein YPD1 affects chloroplast development and leaf senescence.

The expanding and function of NLRC3 or NLRC3-like in teleost fish: Recent advances and novel insights

The nucleotide-binding domain and leucine-rich repeat-containing family (NLR) proteins are innate immune sensors which recognize highly conserved pathogen-associated molecular patterns (PAMPs). Mammals have small numbers of NLR proteins, whereas in some species such as in invertebrates and jawless vertebrates, NLRs have expanded into very large families. Nearly 400 NLR proteins are identified in the zebrafish genome. Members of the NLR family can be divided into two functional sub-groups based on their ability to either positively or negatively regulate host immune response or inflammatory signaling cascades. Mammalian NLRC3 has been identified as an inhibitory NLR, and serves as a negative regulator in the NF-κB-mediated inflammatory response, STING-mediated DNA sensing and PI3K-mTOR pathways. Different from mammalian NLRC3, the analysis from genomes or transcriptomes revealed that the expansions of NLRC3 existed in different species of fish. Furthermore, piscine NLRC3-like genes were confirmed to have a negative or positive regulatory function in response to different kinds of pathogen infections and in the production of proinflammatory cytokines. In this review, we summarize recent advances in our understanding of the expanding and function of NLRC3 or NLRC3-like genes in teleost fish, and give our view of important directions for future studies. The knowledge of piscine NLRC3 or expansive NLRC3-like genes-mediated biological functions in homeostasis and diseases will shed new light on the prevention and control of inflammatory and/or infectious diseases.

NLRC3-like 1 inhibits NOD1-RIPK2 pathway via targeting RIPK2

Both NLRC3 and NOD1 belong to regulatory NLR subfamily based on their best-characterized function. In mammals, NLRC3 was reported to function by attenuating signaling cascades initiated by other families of PRRs. In teleosts, multiple NLRC3-like genes were identified through transcriptome sequencing. However, the functions of many NLRC3-like genes, especially the fish-specific NLRC3-like genes, remain unclear. In the present study, we report the functional characterization of a novel category of NLRC3-like proteins (named as NLRC3-like 1) from the zebrafish, which consists of a fish-specific FISNA, a conserved NACHT and five C-terminal LRRs domains. The expression of zebrafish NLRC3-like 1 was inducible in response to Edwardsiella piscicida infection. During bacterial infection, the in vitro and in vivo studies revealed that zebrafish NLRC3-like 1 overexpression facilitated bacterial growth and dissemination, together with the decreased survival rate of zebrafish larvae infected with E. piscicida. The attenuated response by zebrafish NLRC3-like 1 in response to bacterial infection were characterized by the impaired expression of antibacterial genes, proinflammatory cytokines and Nox genes. Furthermore, zebrafish NLRC3-like 1 interacted with the adaptor protein RIPK2 of NODs signaling via the FISNA (Fish-specific NACHT associated domain) and NACHT domains. However, the interaction between zebrafish NLRC3-like 1 and RIPK2 inhibited the assembly of the NOD1-RIPK2 complex. Importantly, zebrafish NLRC3-like 1 inhibited NOD1-mediated antibacterial activity, NF-κB and MAPK pathways and proinflammatory cytokine production. All together, these results firstly demonstrate that zebrafish NLRC3-like 1 inhibits NOD1-RIPK2 antibacterial pathway via targeting the adaptor protein RIPK2.

De novo assembly and characterization of the liver transcriptome of Mugil incilis (lisa) using next generation sequencing

Mugil incilis (lisa) is an important commercial fish species in many countries, living along the coasts of the western Atlantic Ocean. It has been used as a model organism for environmental monitoring and ecotoxicological investigations. Nevertheless, available genomic and transcriptomic information for this organism is extremely deficient. The aim of this study was to characterize M. incilis hepatic transcriptome using Illumina paired-end sequencing. A total of 32,082,124 RNA-Seq read pairs were generated utilizing the HiSeq platform and subsequently cleaned and assembled into 93,912 contigs (N50 = 2,019 bp). The analysis of species distribution revealed that M. incilis contigs had the highest number of hits to Stegastes partitus (13.4%). Using a sequence similarity search against the public databases GO and KEGG, a total of 7,301 and 16,967 contigs were annotated, respectively. KEGG database showed genes related to environmental information, metabolism and organismal system pathways were highly annotated. Complete or partial coding DNA sequences for several candidate genes associated with stress responses/detoxification of xenobiotics, as well as housekeeping genes, were employed to design primers that were successfully tested and validated by RT-qPCR. This study presents the first transcriptome resources for Mugil incilis and provides basic information for the development of genomic tools, such as the identification of RNA markers, useful to analyze environmental impacts on this fish Caribbean species.

Characterization of class B scavenger receptor type 1 (SRB1) in turbot (Scophthalmus maximus L.)

Class B scavenger receptor type 1 (SRB1) serves as a high-density lipoprotein (HDL) receptor essential for HDL metabolism, and plays vital roles in innate immunity. In this study, the turbot (Scophthalmus maximus) SRB1 was cloned and characterized. The gene structure consists of a coding region of 1,527 bp nucleotides dividing into 13 exons and 12 introns. Such genome structure is highly conserved among teleost fishes. The deduced SRB1 encodes 508 amino acids that mainly has a CD36 transmembrane domain. Tissue distribution of SRB1 showed the lowest expression in liver, while the highest expression was found in intestine. Significantly down-regulation pattern of SmSRB1 expression in intestine was shared after infection with Vibrio anguillarum and Streptococcus iniae. Brach and site models in CODEML program showed that SmSRB1 underwent a conservative evolutionary and three potential positive selected sites 470K, 496E, and 501Y were detected, which requires further investigation and confirmation using base-editing technologies. Subcellular localization demonstrated that turbot SRB1 was distributed in the membrane and cytoplasm. rSmSRB1 showed binding ability in vitro to bacteria, LPS, PGN, LTA and virus. Protein-protein interaction network agrees the function of SRB1 as lipoprotein receptor. Our results indicated SmSRB1 might act as co-receptors to TLRs and NLRs to modulate the immune response to pathogens. Further studies should pay attention to evaluate the specific co-receptor for SRB1 in recognition of different pathogens and selective mechanisms involved.

Identification and initial functional characterization of lysosomal integral membrane protein type 2 (LIMP-2) in turbot (Scophthalmus maximus L.)

The immune system protects organism from external pathogens, this progress starts with the pathogen recognition by pattern recognition receptors (PRRs). As a group of PRRs, the class B scavenger receptors showed important roles in phagocytosis. Among three class B scavenger receptors, lysosomal integral membrane protein type 2 (LIMP-2) was reported to present in the limiting membranes of lysosomes and late endosomes, but its immune roles in teleost species are still limited in handful species. Here, we characterized LIMP-2 gene in turbot, and its expression patterns in mucosal barriers following different bacterial infection, as well as ligand binding activities to different microbial ligands and agglutination assay with different bacteria. In our results, one SmLIMP2 gene was identified with a 1,593 bp open reading frame (ORF). The multiple species comparison and phylogenetic analysis showed the closest relationship to Paralichthys olivaceus, the genomic structure analysis and syntenic analysis revealed the conservation of LIMP-2 during evolution. In tissue distribution analysis, SmLIMP-2 was expressed in all the examined turbot tissues, with the highest expression level in brain, and the lowest expression level in liver. In addition, SmLIMP-2 was significantly up-regulated in all the mucosal tissues (skin, gill and intestine) following Gram-negative bacteria Vibrio anguillarum infection, and was only up-regulated in gill following Gram-positive bacteria Streptococcus iniae challenge. Finally, the rSmLIMP-2 showed strong binding ability to all the examined microbial ligands, and strong agglutination with Escherichia coli, Staphylococcus aureus and V. anguillarum. Taken together, our results suggested SmLIMP-2 played important roles in fish immune response to bacterial infection. However, further functional studies should be carried out to better characterize its detailed roles in teleost immunity.

Identification of a fish-specific NOD-like receptor subfamily C (NLRC) gene from common carp (Cyprinus carpio L.): Characterization, ontogeny and expression analysis in response to immune stimulation

Nucleotide-binding oligomerization domain (NOD)-like receptors (NLRs) are a large group of cytoplasmic pattern recognition receptors (PRRs), which play an important role in pathogen recognition and regulation of innate immune response. In fish, NLRs are divided into three distinct subfamilies: NLR-A resembling mammalian NODs, NLR-B resembling mammalian NALPs and fish-specific NLR-C. Presently, no data is available about the common carp NLR gene, and meanwhile the studies concerning fish NLR-C subfamily genes are relatively poor. In the present study, we cloned and characterized a novel NLRC gene (CcNLRC) from common carp. The full-length cDNA of CcNLRC was 3642 bp, with an ORF of 3078 bp encoding 1025 amino acids. CcNLRC appears to be unique to fish, consisting of a fish-specific NACHT associated (FISNA) domain, a NACHT domain, three LRR motifs and an extra B30.2 domain at C-terminus. Expression analysis revealed that CcNLRC was constitutively expressed in various healthy tissues, and during early developmental stages CcNLRC had two expression peaks (1 dpf and 24 dpf). In vivo stimulation with polyI:C and V. anguillarum showed significant up-regulation of CcNLRC expression in some immune-related tissues including liver, spleen, foregut, hindgut and skin. Additionally, in vitro study in common carp PBLs and HKLs stimulated with different ligands such as polyI:C, flagellin and PGN showed enhanced gene expression of CcNLRC. These results suggested that CcNLRC might play an important role in the innate immune defense of common carp against pathogen invasion.

Expression profiling and functional characterization of CD36 in turbot (Scophthalmus maximus L.)

CD36 is a scavenger receptor, a type of membrane-bound receptors that characterized by recognizing a variety of ligands including endogenous proteins and pathogens. Here, we characterized CD36 gene in turbot, and its expression patterns in mucosal barriers following different bacterial infection, as well as microbial ligand binding ability and bacteriostatic activities. In current study, one SmCD36 gene was captured with a 1407 bp open reading frame (ORF). In multiple species comparison, SmCD36 showed the highest similarity and identity to Cynoglossus semilaevis. In the phylogenetic analysis, SmCD36 showed the closest relationship to C. semilaevis, followed by Takifugu rubripes. The genomic structure analysis showed that CD36 had 12 exons with almost the same length in vertebrate species, indicating the conservation of CD36 during evolution. The syntenic analysis revealed that CD36 located between GNAI1 and SEMA3C genes across all the selected species, which suggested the synteny encompassing CD36 region during vertebrate evolution. Subsequently, SmCD36 was expressed in all the examined turbot tissues, with the highest expression level in intestine. In addition, SmCD36 was significantly up-regulated in intestine following both Gram-negative bacteria Vibrio anguillarum, and Gram-positive bacteria Streptococcus iniae immersion challenge. Finally, the rSmCD36 showed strong binding ability to all the examined microbial ligands and significant inhibition effect on Staphylococcus aureusrequires. Taken together, our results suggested SmCD36 involved in fish innate immune responses to bacterial infection. However, the knowledge of CD36 are still limited in teleost species, further studies should be carried out to better characterize its detailed roles in teleost mucosal immunity.

Nucleotide-binding and oligomerization domain (NOD)-like receptors in teleost fish: Current knowledge and future perspectives

Nucleotide-binding and oligomerization domain (NOD)-like receptors (NLRs) are a group of intracellular pathogen recognition receptors (PRRs) that play key roles in pathogen recognition and subsequent activation of innate immune signalling pathways. Expressions of several NLR subfamily members, including NOD1, NOD2, NLR-C3, NLR-C5 and NLR-X1 have been reported in many different teleost fish species. These receptors are activated by a variety of ligands, including lipopolysaccharides (LPS), peptidoglycans (PGN) and polyinosinic-polycytidylic acid [Poly(I:C)]. Synthetic dsRNA and bacterial or viral infections are known to stimulate these receptors both in vitro and in vivo. In this review, we focus on the identification, expression and function of teleost NLRs in response to bacterial or viral pathogens. Additionally, NLR ligand specificity and signalling pathways involved in the recognition of bacterial or viral stimuli are also summarized. This review focuses on current knowledge in this area and provides future perspectives regarding topics in need of additional investigation. Understanding the response of innate immune system to bacterial or viral infections in diverse species could inform the development of more effective therapies and vaccines.

l-rhamnose-binding lectins (RBLs) in turbot (Scophthalmus maximus L.): Characterization and expression profiling in mucosal tissues

Rhamnose-binding lectin (RBL) were mostly identified from egg cortex and ovary cells from vertebrates and invertebrates, with the specific binding activities to l-rhamnose or d-galactose. Previously, we found that a RBL gene was dramatically down-regulated (-11.90 fold at 1 h, -48.95 fold at 4 h, -905.94 fold at 12 h) in the intestine of turbot following Vibrio anguillarum challenge using RNA-seq expression analysis. In this regard, we sought here to identify RBLs in turbot, as well as the analysis of genomic structure, phylogenetic relationships, basal tissue distribution and the expression patterns following different bacteria challenge in mucosal tissues. In this study, two RBLs were captured in turbot with two conserved type 5 CRD5s, which were belong to type IIIc RBL. In phylogenetic tree analysis, turbot RBLs were clustered with tilapia, European sea bass and snakehead. In addition, in comparison of genomic architecture of turbot RBLs with the available published RBL genes revealed a high degree of conservation in the exon/intron organization among the teleost species. Moreover, both RBLs were significantly up-regulated in mucosal tissues following V. anguillarum and Streptococcus iniae challenge, indicated their critical roles in turbot mucosal immunity. Further studies are needed to expand functional characterization of detailed mechanisms of RBLs in fish innate immunity.

Reprint of: Environmental toxicology and omics: A question of sex

Molecular initiating events and downstream transcriptional/proteomic responses provide valuable information for adverse outcome pathways, which can be used predict the effects of chemicals on physiological systems. There has been a paucity of research that addresses sex-specific expression profiling in toxicology and due to cost, time, and logistic considerations, sex as a variable has not been widely considered. In response to this deficiency, federal agencies in the United States, Canada, and Europe have highlighted the importance of including sex as a variable in scientific investigations. Using case studies from both aquatic and mammalian toxicology, we report that there can be less than ~20-25% consensus in how the transcriptome and proteome of each sex responds to chemicals. Chemicals that have been shown to elicit sex-specific responses in the transcriptome or proteome include pharmaceuticals, anti-fouling agents, anticorrosive agents, and fungicides, among others. Sex-specific responses in the transcriptome and proteome are not isolated to whole animals, as investigations demonstrate that primary cell cultures isolated from each sex responds differently to toxicants. This signifies that sex is important, even in cell lines. Sex has significant implications for predictive toxicology, and both male and female data are required to improve robustness of adverse outcome pathways.

BIOLOGICAL SIGNIFICANCE

Clinical toxicology recognizes that sex is an important variable, as pharmacokinetics (ADME; absorption, distribution, metabolism, and excretion) can differ between females and males. However, few studies in toxicology have explored the implication of sex in relation to the transcriptome and proteome of whole organisms. High-throughput molecular approaches are becoming more frequently applied in toxicity screens (e.g. pre-clinical experiments, fish embryos, cell lines, synthetic tissues) and such data are expected to build upon reporter-based cell assays (e.g. receptor activation, enzyme inhibition) used in toxicant screening programs (i.e. Tox21, ToxCast, REACH). Thus, computational models can more accurately predict the diversity of adverse effects that can occur from chemical exposure within the biological system. Our studies and those synthesized from the literature suggest that the transcriptome and proteome of females and males respond quite differentially to chemicals. This has significant implications for predicting adverse effects in one sex when using molecular data generated in the other sex. While molecular initiating events are not expected to differ dramatically between females and males (i.e. an estrogen binds estrogen receptors in both sexes), it is important to acknowledge that the downstream transcriptomic and proteomic responses can differ based upon the presence/absence of co-regulators and inherent sex-specific variability in regulation of transcriptional and translational machinery. Transcriptomic and proteomic studies also reveal that cell processes affected by chemicals can differ due to sex, and this can undoubtedly lead to sex-specific physiological responses.

Characterization and functional assessment of the NLRC3-like molecule of the goldfish (Carassius auratus L.)

The NLRC3-like (NLRC3L) molecule from the goldfish transcriptome database was identified and characterized. Quantitative gene expression analysis revealed the highest mRNA levels of NLRC3L were in the spleen and intestine, with lower mRNA levels observed in muscle and liver. Goldfish NLRC3L was differentially expressed in goldfish immune cell populations with highest mRNA levels measured in PBLs and macrophages. We generated a recombinant form of the molecule (rgfNLRC3L) and an anti-CT-NLRC3L IgG. Treatment of goldfish primary kidney macrophages in vitro with ATP, LPS and heat-killed Aeromonas salmonicida up-regulated the NLRC3L mRNA and protein. Confocal microscopy and co-immunoprecipitation assays indicated that goldfish rgfNLRC3L interacted with apoptosis-associated spec-like protein (ASC) in eukaryotic cells, indicating that NLRC3L may participate in the regulation of the inflammasome responses. The dual-luciferase reporter assay showed that NLRC3L over-expression did not cause the activation of NF-κB, but that it cooperated with RIP2 to down-regulate NF-κB activation. Our results indicate that the NLRC3L may function as a regulator of NLR pathways in teleosts.

Molecular characterization, expression and functional analysis of NOD1, NOD2 and NLRC3 in Nile tilapia (Oreochromis niloticus)

The nucleotide-binding oligomerization domain proteins NOD1, NOD2 and NLRC3 are cytoplasmic pattern recognition receptors (PRRs) of the Nod-like receptor (NLR) family. In the present study, the Nile tilapia (Oreochromis niloticus) NOD1 (ntNOD1), NOD2 (ntNOD2) and NLRC3 (ntNLRC3) genes were cloned and characterized. The full-length ntNOD1, ntNOD2 and ntNLRC3 genes were 3924, 3886 and 4574 bp, encoding 941, 986 and 1130 amino acids, respectively. The three Nod-like receptors have a NACHT domain and a C-terminal leucine-rich repeat (LRR) domain. In addition, ntNOD1 and ntNOD2 have a N-terminal CARD domain (ntNOD2 has two). Phylogenetic analysis showed that the three NLRs are highly conserved. Tissue expression analysis of the three receptors revealed that the highest mRNA and protein levels of ntNOD1, ntNOD2 and ntNLRC3 were in the spleen. The expression patterns of NLRs during embryonic development showed that the expression levels of ntNOD2 and ntNLRC3 significantly increased from 2 to 8 days post-fertilization (dpf). The expression levels of ntNOD1 significantly increased from 2 to 6 dpf, decreased at 7 dpf and then increased at 8 dpf. Upon stimulation with an intraperitoneal injection of Streptococcus agalactiae, expression levels of the ntNOD1, ntNOD2 and ntNLRC3 mRNA and protein were clearly altered in the blood, spleen, kidney, intestine and gill. Furthermore, after cotransfection with an NF-κB reporter plasmid, NF-κB activation in ntNOD1-overexpressing 293T cells significantly increased compared with that in control cells, before or after i-EDPA-stimulation. By contrast, compared with control, ntNOD2 and ntNLRC3 had no effect on NF-κB activation in 293T cells, when their potential ligands were not stimulated. However, after MDP-stimulation, ntNOD2 and ntNLRC3 overexpression increased NF-κB activation in 293T cells. NOD1 and NLRC3 were uniformly distributed throughout the cytoplasm in 293T cells, whereas NOD2 was distributed throughout the cytoplasm and nucleus. Our results indicate that the three Nod-like receptors are functionally conserved and may play pivotal roles in defense against pathogens such as Streptococcus agalactiae.

Alternative Pre-mRNA Splicing in Mammals and Teleost Fish: A Effective Strategy for the Regulation of Immune Responses Against Pathogen Infection

Pre-mRNA splicing is the process by which introns are removed and the protein coding elements assembled into mature mRNAs. Alternative pre-mRNA splicing provides an important source of transcriptome and proteome complexity through selectively joining different coding elements to form mRNAs, which encode proteins with similar or distinct functions. In mammals, previous studies have shown the role of alternative splicing in regulating the function of the immune system, especially in the regulation of T-cell activation and function. As lower vertebrates, teleost fish mainly rely on a large family of pattern recognition receptors (PRRs) to recognize pathogen-associated molecular patterns (PAMPs) from various invading pathogens. In this review, we summarize recent advances in our understanding of alternative splicing of piscine PRRs including peptidoglycan recognition proteins (PGRPs), nucleotide binding and oligomerization domain (NOD)-like receptors (NLRs), retinoic acid-inducible gene-I (RIG-I)-like receptors (RLRs) and their downstream signaling molecules, compared to splicing in mammals. We also discuss what is known and unknown about the function of splicing isoforms in the innate immune responses against pathogens infection in mammals and teleost fish. Finally, we highlight the consequences of alternative splicing in the innate immune system and give our view of important directions for future studies.