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(A) The ME tree of the amphioxus TNF family. Both alleles are included in the analysis. (Bf) B. floridae. (B) The configuration of the TNF cluster on Scaffold_7. Gray ovals indicate genes with expression data (Supplemental Fig. S9).
Source publication
It has been speculated that before vertebrates evolved somatic diversity-based adaptive immunity, the germline-encoded diversity of innate immunity may have been more developed. Amphioxus occupies the basal position of the chordate phylum and hence is an important reference to the evolution of vertebrate immunity. Here we report the first comprehen...
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Context 1
... analysis of the TNF domain indicates that am- phioxus TNF proteins can be separated into two major lineages, the TRAIL/FASLG-related and the EDA/Eiger-related lineages ( Fig. 5A; Supplemental Fig. S8). The TRAIL/FASLG-related lineage in- cludes 10 TRAIL genes and three FASLG/TNFA-like genes, whereas the EDA/Eiger-related lineage contains 11 TNF genes ho- mologous to insect Eiger, vertebrate EDA, and TNFSF13. Amphi- oxus TRAIL proteins share 45%-58% amino acid identity with vertebrate TRAILs, whereas the FASLG/TNFA-like proteins ...
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... amino acid similarity with vertebrate FASLG or TNFA. In addition, an amphioxus TNF is clustered with vertebrate CD40LG, but the sequence similarity is rather weak. There is a TNF cluster of 12 genes located on the Scaffold_7, comprising five EDA/Eiger-related TNFs in the middle, six TRAIL/FASLG-related TNFs on one side, and one on the other side (Fig. 5B). Together with the phylogenetic analysis, this genomic configuration pro- vides an update to the evolutionary story of vertebrate TNFs (Collette et al. 2003). The TRAIL/FASLG-related lineage was first cre- ated by tandem duplication from the ancient EDA/Eiger-related lineage and then underwent substantial functional divergence before ...
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... functional divergence before whole-genome duplications; later, in the early evolution of vertebrates, whole-genome duplications produced TNFSF11, LTA, and TNFSF15 from the ancient TRAIL/FASLG-related lin- eage, and produced TNFSF13 and TNFSF13B from the ancient EDA/Eiger-related lineage. We have cloned cDNAs for five TRAILs from B. japonicum (Fig. 5A,B, marked by gray ovals). Initial analy- sis indicates that they assume disparate expression patterns in different tissues, suggesting that these TRAIL proteins may have achieved substantial functional divergence after rapid lineage- specific duplications (Supplemental Fig. ...
Citations
... The significant success of the adaptive immune system has been achieved by acquisition of vertebrate-specific molecules, including major histocompatibility complexes (MHCs), T-cell receptors (TCRs), and immunoglobulins (Igs) [1]. On the other hand, some invertebrates have evolved a wide variety of recognition (e.g., receptors of non-self antigens) and effector molecules (e.g., signaling molecules, complement systemrelated, antimicrobial peptides (AMPs), etc.) via genome-wide expansion or diversification of innate immune-related genes in a species-specific manner [7][8][9][10][11]. ...
A wide variety of bioactive peptides have been identified in the central nervous system and several peripheral tissues in the ascidian Ciona intestinalis type A (Ciona robusta). However, hemocyte endocrine peptides have yet to be explored. Here, we report a novel 14-amino-acid peptide, CiEMa, that is predominant in the granular hemocytes and unilocular refractile granulocytes of Ciona. RNA-seq and qRT-PCR revealed the high CiEma expression in the adult pharynx and stomach. Immunohistochemistry further revealed the highly concentrated CiEMa in the hemolymph of the pharynx and epithelial cells of the stomach, suggesting biological roles in the immune response. Notably, bacterial lipopolysaccharide stimulation of isolated hemocytes for 1–4 h resulted in 1.9- to 2.4-fold increased CiEMa secretion. Furthermore, CiEMa-stimulated pharynx exhibited mRNA upregulation of the growth factor (Fgf3/7/10/22), vanadium binding proteins (CiVanabin1 and CiVanabin3), and forkhead and homeobox transcription factors (Foxl2, Hox3, and Dbx) but not antimicrobial peptides (CrPap-a and CrMam-a) or immune-related genes (Tgfbtun3, Tnfa, and Il17-2). Collectively, these results suggest that CiEMa plays roles in signal transduction involving tissue development or repair in the immune response, rather than in the direct regulation of immune response genes. The present study identified a novel Ciona hemocyte peptide, CiEMa, which paves the way for research on the biological roles of hemocyte peptides in chordates.
... An expanded superfamily of 218 SRCR-SF models in the sea urchin [30] was first reported. Subsequently, the expansion of SRCR-SFs was also identified in the Pacific oyster (Crassostrea gigas) [31] and the amphioxus (Branchiostoma floridae) [32]. Examination of SRCR-SFs in the scallop Chlamys farreri revealed their involvement in immune responses, not only to bacterial invasion but also to fungal invasion [33]. ...
Without general adaptative immunity, invertebrates evolved a vast number of heterogeneous non-self recognition strategies. One of those well-known adaptations is the expansion of the immune receptor gene superfamily coding for scavenger receptor cysteine-rich domain containing proteins (SRCR) in a few invertebrates. Here, we investigated the evolutionary history of the SRCR gene superfamily (SRCR-SF) across 29 metazoan species with an emphasis on invertebrates. We analyzed their domain architectures, genome locations and phylogenetic distribution. Our analysis shows extensive genome-wide duplications of the SRCR-SFs in Amphimedon queenslandica and Strongylocentrotus purpuratus. Further molecular evolution study reveals various patterns of conserved cysteines in the sponge and sea urchin SRCR-SFs, indicating independent and convergent evolution of SRCR-SF expansion during invertebrate evolution. In the case of the sponge SRCR-SFs, a novel motif with seven conserved cysteines was identified. Exon–intron structure analysis suggests the rapid evolution of SRCR-SFs during gene duplications in both the sponge and the sea urchin. Our findings across nine representative metazoans also underscore a heightened expression of SRCR-SFs in immune-related tissues, notably the digestive glands. This observation indicates the potential role of SRCR-SFs in reinforcing distinct immune functions in these invertebrates. Collectively, our results reveal that gene duplication, motif structure variation, and exon–intron divergence might lead to the convergent evolution of SRCR-SF expansions in the genomes of the sponge and sea urchin. Our study also suggests that the utilization of SRCR-SF receptor duplication may be a general and basal strategy to increase immune diversity and tissue specificity for the invertebrates.
... The increased production of IL6, IL18, IL1β, or TNFs was used as key indicator for the detection of trained immunity in vertebrates [12,48,49]. Some cytokines such as IL17s [31], TNFs [50], and interferons have been identified in C. gigas [29,51,52]. There are ten IL17 genes annotated from the genome of C. gigas, which are p < 0.05, and 4.18-fold, p < 0.01, compared with the DMSO group, respectively), while the mRNA transcripts of CgRel1 showed no significant change ( Figure 6). ...
... The increased production of IL6, IL18, IL1β, or TNFs was used as key indicator for the detection of trained immunity in vertebrates [12,48,49]. Some cytokines such as IL17s [31], TNFs [50], and interferons have been identified in C. gigas [29,51,52]. There are ten IL17 genes annotated from the genome of C. gigas, which are ...
... The increased production of IL6, IL18, IL1β, or TNFs was used as key indicator for the detection of trained immunity in vertebrates [12,48,49]. Some cytokines such as IL17s [31], TNFs [50], and interferons have been identified in C. gigas [29,51,52]. There are ten IL17 genes annotated from the genome of C. gigas, which are considered to play diverse roles in immune defense [30]. ...
Increasing evidence confirms that histone modification plays a critical role in preserving long-term immunological memory. Immune priming is a novel form of immunological memory recently verified in invertebrates. Toll-like receptor (TLR) signaling and cytokines have been reported to be involved in the immune priming of the Pacific oyster Crassostrea gigas. In the present study, the expression of Toll-like receptor 3 (CgTLR3), myeloid differentiation factor 88-2 (CgMyd88-2) and interleukin 17-1 (CgIL17-1) was found to be elevated in the hemocytes of C. gigas at 6 h after the secondary stimulation with Vibrio splendidus, which was significantly higher than that at 6 h after the primary stimulation (p < 0.05). A significant increase in histone H3 lysine 4 trimethylation (H3K4me3) enrichment was detected in the promoter region of the CgTLR3 gene at 7 d after the primary stimulation with inactivated V. splendidus (p < 0.05). After the treatment with a histone methyltransferase inhibitor (5′-methylthioadenosine, MTA), the level of H3K4me3 at the promoter of the CgTLR3 gene decreased significantly at 7 d after the primary stimulation with inactivated V. splendidus (p < 0.05), and the expression of CgTLR3, CgMyD88-2 and CgIL17-1 was significantly repressed at 6 h after the secondary stimulation with V. splendidus (p < 0.05). Conversely, the treatment with monomethyl fumarate (MEF, an inhibitor of histone demethylases) resulted in a significant increase in H3K4me3 enrichment levels at the CgTLR3 promoter at 7 d after the primary stimulation (p < 0.05), and the expression of CgTLR3, CgMyD88-2 and CgIL17-1 was observed to increase significantly at 6 h after the secondary stimulation (p < 0.05). These results suggested that H3K4me3 regulated MyD88-dependent TLR signaling in the hemocytes of C. gigas, which defined the role of histone modifications in invertebrate immune priming.
... The significant success of the adaptive immune system hypothesizes the reduction of the molecular variation of the innate immune system in vertebrates [1]. On the other hand, some invertebrates have evolved a wide variety of recognition and effector molecules via genome-wide expansion or diversification of innate immune-related genes in a species-specific manner [2][3][4][5]. ...
A wide variety of bioactive peptides have been identified in the central nervous system and several peripheral tissues in the ascidian Ciona intestinalis type A (Ciona robusta). However, hemocyte endocrine peptides have yet to be explored. Here, we report a novel 14-amino acid peptide, CiEMa, that is predominant in the granular hemocytes and unilocular refractile granulocytes of Ciona. RNA-seq and qRT-PCR revealed the high CiEma expression in the adult pharynx and stomach. Immunohistochemistry further revealed the highly concentrated CiEMa in the hemolymph of the pharynx and epithelial cells of the stomach, suggesting biological roles in the immune response. Notably, bacterial lipopolysaccharide stimulation of isolated hemocytes for 1-4 hours resulted in increased CiEMa secretion. Furthermore, CiEMa-stimulated pharynx exhibited mRNA upregulation of the growth factor (Fgf3/7/10/22), vanadium binding proteins (CiVanabin1 and CiVanabin3), and forkhead and homeobox transcription factors (Foxl2, Hox3, and Dbx), but not antimicrobial peptides (CrPap-a and CrMam-a) or immune-related genes (Tgfbtun3, Tnfa, and Il17-2). Collectively, these results suggest that CiEMa plays roles in signal transduction involving tissue development or repair in the immune response, rather than in the direct regulation of immune-response genes. The present study identified a novel Ciona hemocyte peptide, CiEMa, providing insights into the molecular and functional diversity of the immune response in chordates.
... The expansion of the TLRs in fish is especially noteworthy. TLRs with large copy numbers have been identified in distantly related lineages to G. morhua, such as sea urchins and chordates, which contain 222 and 77 TLRs, respectively, and they were studied in connection to these species' lack of a particular adaptive immune system (Rast et al., 2006;Huang et al., 2008). The TLR gene expansion and isoform acquisition in G. morhua have been linked to the extremely varied pathogen loads and community composition of paleoclimatic Arctic environments (Solbakken et al., 2016). ...
The Patagonian moray cod, Muraenolepis orangiensis, belongs to the family Muraenolepididae and is the sole order of Gadiformes that inhabits the temperate and cold waters of the southern hemisphere. One of the features of the Gadiformes order is that they have a remarkably unique immune gene repertoire that influences innate and adaptive immunity, and they lack major histocompatibility complex (MHC) class II, invariant chains (CD74), and CD4 genes. In this study, a high-quality chromosome-level genome assembly was constructed, resulting in a final assembled genome of 893.75 Mb, with an N50 scaffold length of 30.07 Mb and the longest scaffold being 39.77 Mb. Twenty-five high-quality pseudochromosomes were assembled, and the complete BUSCO rate was 93.4%. A total of 34,553 genes were structurally annotated, and 27,691 genes were functionally annotated. Among the 10 primary genes involved in MHC class II, only two ERAP1 genes and one AIRE gene were identified through the genome study. Although no specific reason for the MHC class II deficiency has been identified, it has been shown that the toll-like receptors (TLRs), which are significant to the innate immune response, are significantly expanded in M. orangiensis. A total of 44 TLRs have been identified, with 32 TLR13 genes distributed evenly on six different pseudochromosomes. This study is the first to reveal the whole genome of a Muraenolepididae family and provides valuable insights into the potential rationale for the MHC class II deficiency in a Gadiformes fish species.
... It was evaluated with alanine replacement and deletion mutagenesis to explore the relative contributions of the leucine residues that can export nuclear protein. The LRR domain is confined to microbial proteins and it is correlated with innate immunity [194]. LRR-containing proteins are also closely linked with numerous cellular mechanisms, including apoptosis, ubiquitin-related progressions, and nuclear mRNA passage [195,196]. ...
Infectious bronchitis virus (IBV) is an avian coronavirus (CoV) that belongs to the genus Gammacoronavirus and has been listed as an important disease by the World Organization for Animal Health (WOAH). It causes highly contagious respiratory, reproductive, and renal diseases in commercial poultry farms. Multiple IBV serotypes and genotypes have been identified in many countries and many detected variants do not provide cross-protection against infection, resulting in repeated outbreaks and significant economic losses worldwide. In addition, the high genetic mutations and recombination events in the prominent genomic regions of IBV, particularly in the spike glycoprotein (S) and nucleocapsid (N) proteins, are directly involved in the evolutionary processes of IBV and lead to increased pathogenicity and tissue tropism. The characterization of the different genotypes and the relationship between the structure, function, post-translational modifications (PTMs), and structural motifs will elucidate the mechanisms that promote replication and pathogenicity and affect the host’s immune response during infection. In this review, we discuss the molecular features of various IBV genes and proteins that contribute to the infection process. We also highlight the common PTMs and structural motifs that occur during protein synthesis and are essential components of IBV ecology.
... The amphioxus (Branchiostoma belcheri) is a marine filter-feeding animal that generally lives in sandy, shallow habitats in tropical and temperate ocean areas [27]. Amphioxi are located at the base in the chordata, and they have been regarded as important in the study of the origin of chordates [28]. For this work, we cloned a new VLDLR gene homolog in amphioxi (designated as AmphiVLDLR). ...
Low-density lipoprotein receptors (LDLRs) are a class of cell-surface endocytosis receptors that are mainly involved in cholesterol homeostasis and cellular signal transduction. Very-low-density lipoprotein receptors (VLDLRs), which are members of the LDLR family, have been regarded as multi-function receptors that fulfill diverse physiological functions. However, no VLDLR gene has been identified in protochordates to date. As a representative protochordate species, amphioxi are the best available example of vertebrate ancestors. Identifying and characterizing the VLDLR gene in amphioxi has high importance for exploring the evolutionary process of the LDLR family. With this study, a new amphioxus VLDLR gene (designated AmphiVLDLR) was cloned and characterized using RACE-PCR. The 3217 nt transcript of the AmphiVLDLR had a 2577 nt ORF, and the deduced 858 amino acids were highly conserved within vertebrate VLDLRs according to their primary structure and three-dimensional structure, both of which contained five characteristic domains. In contrast to other vertebrate VLDLRs, which had a conserved genomic structure organization with 19 exons and 18 introns, the AmphiVLDLR had 13 exons and 12 introns. The results of a selective pressure analysis showed that the AmphiVLDLR had numerous positive selection sites. Furthermore, the tissue expression of AmphiVLDLR using RT-qPCR showed that AmphiVLDLR RNA expression levels were highest in the gills and muscles, moderate in the hepatic cecum and gonads, and lowest in the intestines. The results of the evolutionary analysis demonstrated that the AmphiVLDLR gene is a new member of the VLDLR family whose family members have experienced duplications and deletions over the evolutionary process. These results imply that the functions of LDLR family members have also undergone differentiation. In summary, we found a new VLDLR gene homolog (AmphiVLDLR) in amphioxi. Our results provide insight into the function and evolution of the LDLR gene family.
... In our previous study, we have found gene expansion and dynamic exon shuffling of many immune-related genes in amphioxus [34]. Amphioxus has more than 40 CASPs, including inflammatory CASPs, apoptosis initiator and effector CASPs [35]. ...
... Since EIB202 is an intracellular bacterium (S8D Fig), we thought that the Caspase-GSDME signaling should be activated by the infection of intracellular bacteria or the recognition of intracellular LPS. Although there are up to 92 NLR genes and 45 CASPs in amphioxus due to the expansion of innate immune-related genes [34], how intracellular LPS is recognized is still unclear at present. After sequence analyses, we believed that an inflammasome-like complex may be formed by some BbNLRs, BbCaspase1/2, BbASCs based on the death effector domain (DED) interaction in amphioxus (S8E Fig). ...
Members of the gasdermin (GSDM) family are pore-forming effectors that cause membrane permeabilization and pyroptosis, a lytic proinflammatory type of cell death. To reveal the functional evolution of GSDM-mediated pyroptosis at the transition from invertebrates to vertebrates, we conducted functional characterization of amphioxus GSDME (BbGSDME) and found that it can be cleaved by distinct caspase homologs, yielding the N253 and N304 termini with distinct functions. The N253 fragment binds to cell membrane, triggers pyroptosis, and inhibits bacterial growth, while the N304 performs negative regulation of N253-mediated cell death. Moreover, BbGSDME is associated with bacteria-induced tissue necrosis and transcriptionally regulated by BbIRF1/8 in amphioxus. Interestingly, several amino acids that are evolutionarily conserved were found to be important for the function of both BbGSDME and HsGSDME, shedding new lights on the functional regulation of GSDM-mediated inflammation.
... TLRs, as innate immune-recognition receptors with a solenoidlike LRRNT-LRR-LRRCT ectodomain for ligand recognition, play a critical role in innate immune responses by recognition of microbial pathogens [91,92] Previous studies had revealed that individual TLRs combine with different adapters, such as MyD88, TIRAP, and TRIF, to drive a specific immune response [93]. ...
... Nod-like receptors (NLRs), as a group of intracellular PRRs, have shown a canonical role in the host's fight against pathogens. In vertebrates, NLRs consists of N-terminal domains for signaling, a Cterminal LRR region for ligand recognition, and a central NACHT domain for oligomerization [91,132]. However, NLRs have not been systematically described in lophotrochozoans. ...
... Tumor necrosis factor α (TNFα) is a critical cytokine that consists of various transmembrane proteins with a homologous TNF domain [225]. It contributes to the proliferation, differentiation, and homeostasis of immunocytes, which is involved in the innate and adaptive immune systems [91,225,226]. In molluscans, the first TNFα homolog was characterized in disk abalone, which was significantly up-regulated expressed with the challenge of bacteria, viralhaemorrhagic septicemia virus (VHSV) and lipopolysaccharide (LPS), indicated its role in response to pathogenic infection or stimulation [227]. ...
Lophotrochozoa is one of the most species-rich but immunologically poorly explored phyla. Although lack of acquired response in a narrow sense, lophotrochozoans possess various genetic mechanisms that enhance the diversity and specificity of innate immune system. Here, we review the recent advances of comparative immunology studies in lophotrochozoans with focus on immune recognition and effector systems. Haemocytes and coelomocytes are general important yet understudied player. Comparative genomics studies suggest expansion and functional divergence of lophotrochozoan immune reorganization systems is not as “homogeneous and simple” as we thought including the large-scale expansion and molecular divergence of pattern recognition receptors (PRRs) (TLRs, RLRs, lectins, etc.) and signaling adapters (MyD88s etc.), significant domain recombination of immune receptors (RLR, NLRs, lectins, etc.), extensive somatic recombination of fibrinogenrelated proteins (FREPs) in snails. Furthermore, there are repeatedly identified molecular mechanisms that generate immune effector diversity, including high polymorphism of antimicrobial peptides and proteins (AMPs), reactive oxygen and nitrogen species (RONS) and cytokines. Finally, we argue that the next generation omics tools and the recently emerged genome editing technicism will revolutionize our understanding of innate immune system in a comparative immunology perspective.
... These proteins regulate molecular traffic between the plasma membrane and endosome [65]. TLRs contain the consensus 'Leu-x-x-Leu-x-Leu-x-x-Arg' protein-protein interaction module or the LRR domain [66], which are conserved across species and specifically enriched in plants [67], invertebrates [68], and cephalochordates [69]. The large repertoire of TLRs in animals is attributed to their role in the recognition of pathogens, leading to the development of diverse innate immune signaling cascades. ...
Background
Dung beetles recycle organic matter through the decomposition of feces and support ecological balance. However, these insects are threatened by the indiscriminate use of agrochemicals and habitat destruction. Copris tripartitus Waterhouse (Coleoptera: Scarabaeidae), a dung beetle, is listed as a class-II Korean endangered species. Although the genetic diversity of C. tripartitus populations has been investigated through analysis of mitochondrial genes, genomic resources for this species remain limited. In this study, we analyzed the transcriptome of C. tripartitus to elucidate functions related to growth, immunity and reproduction for the purpose of informed conservation planning.
Results
The transcriptome of C. tripartitus was generated using next-generation Illumina sequencing and assembled de novo using a Trinity-based platform. In total, 98.59% of the raw sequence reads were processed as clean reads. These reads were assembled into 151,177 contigs, 101,352 transcripts, and 25,106 unigenes. A total of 23,450 unigenes (93.40%) were annotated to at least one database. The largest proportion of unigenes (92.76%) were annotated to the locally curated PANM-DB. A maximum of 5,512 unigenes had homologous sequences in Tribolium castaneum. Gene Ontology (GO) analysis revealed a maximum of 5,174 unigenes in the Molecular function category. Further, in Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, a total of 462 enzymes were associated with established biological pathways. Based on sequence homology to known proteins in PANM-DB, representative immunity, growth, and reproduction-related genes were screened. Potential immunity-related genes were categorized into pattern recognition receptors (PRRs), the Toll-like receptor signaling pathway, the MyD88- dependent pathway, endogenous ligands, immune effectors, antimicrobial peptides, apoptosis, and adaptation-related transcripts. Among PRRs, we conducted detailed in silico characterization of TLR-2, CTL, and PGRP_SC2-like. Repetitive elements such as long terminal repeats, short interspersed nuclear elements, long interspersed nuclear elements and DNA elements were enriched in the unigene sequences. A total of 1,493 SSRs were identified among all unigenes of C. tripartitus.
Conclusions
This study provides a comprehensive resource for analysis of the genomic topography of the beetle C. tripartitus. The data presented here clarify the fitness phenotypes of this species in the wild and provide insight to support informed conservation planning.
