VLR-based adaptive immunity

Thermostable lamprey variable lymphocyte receptor antibody for detection of Plasmodium falciparum histidine rich protein-2

Lampreys use variable lymphocyte receptors (VLR) comprising leucine-rich-repeat (LRR) segments for antigen recognition, distinct from immunoglobulin-based receptors of jawed vertebrates. Lamprey VLRs are as diverse and antigen-specific as immunoglobulin-based antibodies, with unique advantages including high avidity, pH stability, and recognition of novel antigen epitopes. Here we describe the generation of VLR monoclonal antibody against histidine rich protein-2 (HRP-2) of Plasmodium falciparum, a causative agent of malaria. HRP-2, expressed by all parasite stages and secreted into plasma, serves as an effective biomarker of infection. Lamprey larvae immunized with purified HRP-2 protein produced specific VLRB antibodies with relatively high serum titers. Using white blood cells from immunized lampreys, we constructed VLR cDNA libraries expressed on yeast surface. Through yeast display screening, we selected recombinant VLRB antibody 5A10 with high affinity and specificity for HRP-2, recognizing both recombinant and native proteins from P. falciparum culture supernatants and infected patient samples. The antibody retains its binding capacity at temperatures up to 70 °C, significantly outperforming a commercial mouse IgG-based anti-HRP-2 antibody. This HRP-2-specific VLR antibody shows promise for improved malaria diagnostics, particularly in tropical regions requiring heat-stable tests.

Live imaging in zebrafish reveals tissue-specific strategies for amoeboid migration

Amoeboid cells such as leukocytes can enter and migrate in diverse tissues, even though tissues vary widely in their chemical and mechanical composition. Here, we imaged motile T cells as they colonized peripheral tissues during zebrafish development to determine whether cells tailor their migration strategy to their local tissue environment. We found that T cells in most sites migrated with F-actin-rich, leading-edge pseudopods, matching how they migrate in vitro. T cells notably deviated from this strategy in the epidermis, where they instead migrated using a rearward concentration of F-actin and stable leading-edge blebs. This mode of migration occurs under planar confinement in vitro, and we found that the stratified keratinocyte layers of the epidermis also impose planar-like confinement on leukocytes in vivo. Collectively, our data indicate that immune cells adapt their migration strategy to navigate different tissue geometries in vivo.

Variable Lymphocyte Receptor B Technologies - Are They Ready for Prime Time?

OBJECTIVE

To review the current and the potential research and clinical use of VLRBs.

METHODS

A literature search was conducted for English studies published in the past 20 years using the terms "Variable Lymphocyte Receptor," "VLR," "VLRB" or "Repebody." Only primary reports were included.

RESULTS

VLRB-based technologies are currently being investigated for diagnosis, imaging, and treatment of diverse conditions including solid organ and hematological malignancies, infectious diseases, autoimmunity, and degenerative and metabolic disorders. VLRB mAbs can be used to directly recognize disease biomarkers, such as B cells from chronic lymphocytic leukemia, or to deliver drugs to the brain or cancer cells. The VLRB C-terminal multimerization domain has been utilized to create vaccines while VLR-based chimeric antigen receptor (CAR) T cell constructs are being investigated for cancer therapies.

CONCLUSIONS

The extensive knowledge gained with VLRB mAbs in diverse in vitro and in vivo models emphasizes their promise for translation into clinical applications and readiness for prime time.

Trained innate immunity: Concept, nomenclature, and future perspectives

During the past decade, compelling evidence has accumulated demonstrating that innate immune cells can mount adaptive characteristics, leading to long-term changes in their function. This de facto innate immune memory has been termed trained immunity. Trained immunity, which is mediated through extensive metabolic rewiring and epigenetic modifications, has important effects in human diseases. Although the upregulation of trained immunity by certain vaccines provides heterologous protection against infections, the inappropriate activation of trained immunity by endogenous stimuli contributes to the pathogenesis of inflammatory and neurodegenerative disorders. Development of vaccines that can induce both classical adaptive immunity and trained immunity may lead to a new generation of vaccines with increased efficacy. Activation of trained immunity can also lead to novel strategies for the treatment of cancer, whereas modulation of trained immunity can provide new approaches to the treatment of inflammatory diseases.

Passive immunoprophylaxis with Ccombodies against Vibrio parahaemolyticus in Pacific white shrimp (Penaeus vannamei)

The Vibrio parahaemolyticus strain causing acute hepatopancreatic necrosis disease (AHPND) in shrimp secretes toxins A and B (PirAVp/PirBVp). These toxins have been implicated in pathogenesis and are targets for developing anti-AHPND therapeutics or prophylactics that include passive immunization. We have previously reported that Ccombodies (recombinant hagfish variable lymphocyte receptor B antibodies; VLRB) targeting PirBVp conferred protection against V. parahaemolyticus in shrimp when administered as a feed supplement. In this study, we screened a phage-displayed library of engineered VLRBs for PirAVp-targeting Ccombodies that were mass-produced in a bacterial expression system. We then introduced these Ccombodies into the diet of Pacific white shrimp (Penaeus vannamei) over a seven-day period. Subsequently, the shrimp were exposed to a challenge with V. parahaemolyticus. Mortality rates were then observed and recorded over the following seven days. Administering shrimp feed supplemented with Ccombodies at a high dose (100 mg per 100 g feed) reduced mortality in recipient animals (2.96-5.19 %) statistically similar to mock-challenged control (1.48 %), but significantly different from the Ccombody-deficient control (74.81 %). This suggests that the Ccombodies provided strong protection against the bacterium. Feeding shrimp with a median dose (10 mg/100 g feed) gave statistically comparable low mortality (5.93-6.67 %) as the high dose. Reducing the Ccombody dose to 1 mg/100 g feed showed variable effects. Ccombody A2 showed mortality (11.85 %) significantly lower than that of the Ccombody-deficient group (74.81 %), suggesting that it can effectively protect against the bacterial challenge at a low dose. Our results demonstrate the ability of the phage-displayed VLRB library to generate antigen-specific Ccombodies rapidly and simply, with the expression of high protein levels in bacteria. The protective effect provided by these Ccombodies aligns with our earlier results, strongly supporting the use of VLRB antibodies as a substitute for IgY in passive immunoprophylaxis against AHPND in shrimp.

Discovery of an unconventional lamprey lymphocyte lineage highlights divergent features in vertebrate adaptive immune system evolution

Lymphocyte receptors independently evolved in both jawed and jawless vertebrates with similar adaptive immune responses. However, the diversity of functional subtypes and molecular architecture in jawless vertebrate lymphocytes, comparable to jawed species, is not well defined. Here, we profile the gills, intestines, and blood of the lamprey, Lampetra morii, with single-cell RNA sequencing, using a full-length transcriptome as a reference. Our findings reveal higher tissue-specific heterogeneity among T-like cells in contrast to B-like cells. Notably, we identify a unique T-like cell subtype expressing a homolog of the nonlymphoid hematopoietic growth factor receptor, MPL-like (MPL-L). These MPL-L+ T-like cells exhibit features distinct from T cells of jawed vertebrates, particularly in their elevated expression of hematopoietic genes. We further discovered that MPL-L+ VLRA+ T-like cells are widely present in the typhlosole, gill, liver, kidney, and skin of lamprey and they proliferate in response to both a T cell mitogen and recombinant human thrombopoietin. These findings provide new insights into the adaptive immune response in jawless vertebrates, shedding new light on the evolution of adaptive immunity.

Live imaging in zebrafish reveals tissue-specific strategies for amoeboid migration

Amoeboid cells like leukocytes can enter and migrate within virtually every tissue of the body, even though tissues vary widely in their chemical and mechanical composition. Here, we imaged motile T cells as they colonized peripheral tissues during zebrafish development to ask if cells tailor their migration strategy to their local tissue environment. We found that T cells in most sites migrated with f-actin-rich leading-edge pseudopods, matching how they migrate in vitro . T cells notably deviated from this strategy in the epidermis, where they instead migrated using a rearward concentration of f-actin and stable leading-edge blebs. This mode of migration occurs under planar confinement in vitro , and we correspondingly found the stratified keratinocyte layers of the epidermis impose planar-like confinement on leukocytes in vivo . By imaging the same cell type across the body, our data collectively indicates that cells adapt their migration strategy to navigate different tissue geometries in vivo .

High throughput long-read sequencing of circulating lymphocytes of the evolutionarily distant sea lamprey reveals diversity and common elements of the variable lymphocyte receptor B (VLRB) repertoire

The leucine-rich repeat-based variable lymphocyte receptor B (VLRB) antibody system of jawless vertebrates is capable of generating an antibody repertoire equal to or exceeding the diversity of antibody repertoires of jawed vertebrates. Unlike immunoglobulin-based immune repertoires, the VLRB repertoire diversity is characterized by variable lengths of VLRB encoding transcripts, rendering conventional immunoreceptor repertoire sequencing approaches unsuitable for VLRB repertoire sequencing. Here we demonstrate that long-read single-molecule real-time (SMRT) sequencing (PacBio) approaches permit the efficient large-scale assessment of the VLRB repertoire. We present a computational pipeline for sequence data processing and provide the first repertoire-based analysis of VLRB protein characteristics including properties of its subunits and regions of diversity within each structural leucine-rich repeat subunit. Our study provides a template to explore changes in the VLRB repertoire during immune responses and to establish large scale VLRB repertoire databases for computational approaches aimed at isolating monoclonal VLRB reagents for biomedical research and clinical applications.

Identification and evolution of PDK-1-like involving lamprey innate immunity

3-phosphoinositide-dependent protein kinase-1 (PDK-1) is a key kinase regulating the activity of the PI3K/AKT pathway and a major regulator of the AGC protein kinase family. It is essential in the physiological activities of cells, embryonic development, individual development and immune response. In this study, we have identified for the first time an analogue of PDK-1 in the most primitive vertebrate, lamprey, and named it PDK-1-like. The protein sequence similarity of lamprey PDK-1-like to human, mouse, chicken, African xenopus and zebrafish PDK-1 were 64.4 %, 64.5 %, 65.0 %, 61.3 % and 63.2 %, respectively. The phylogenetic tree showed that PDK-1-like of lamprey were located at the base of the vertebrate branch, in line with the trend of biological evolution. Meanwhile, homology analysis showed that PDK-1 proteins across species shared a conserved kinase structural domain and a Pleckstrin Homology (PH) domain. Genomic synteny analysis revealed that the large-scale duplication blocks were not found in lamprey genome and neighbor genes of lamprey PDK-1-like presented dramatic differences compared with jawed vertebrates. More importantly, qPCR analysis showed that PDK-1-like was widely expressed in lamprey. Its mRNA expression levels varied in response to different pathogenic stimuli, and its expression was generally up-regulated under Polyinosinic-Polycytidylic acid (Poly(I:C)) stimulation. Pearson's correlation analysis showed that PDK-1-like was involved in co-expressed with MyD88-independent TLR-3 pathway during the immune response of lamprey, instead of MyD88-dependent TLR-3 pathway. In summary, our composite results offer valuable clues to the origin and evolution of PDK-1, and imply that PDK-1 s are among the most ancestral immune regulators in vertebrates.

Trained immunity: General and emerging concepts

Over the past decade, compelling evidence has unveiled previously overlooked adaptive characteristics of innate immune cells. Beyond their traditional role in providing short, non-specific protection against pathogens, innate immune cells can acquire antigen-agnostic memory, exhibiting increased responsiveness to secondary stimulation. This long-term de-facto innate immune memory, also termed trained immunity, is mediated through extensive metabolic rewiring and epigenetic modifications. While the upregulation of trained immunity proves advantageous in countering immune paralysis, its overactivation contributes to the pathogenesis of autoinflammatory and autoimmune disorders. In this review, we present the latest advancements in the field of innate immune memory followed by a description of the fundamental mechanisms underpinning trained immunity generation and different cell types that mediate it. Furthermore, we explore its implications for various diseases and examine current limitations and its potential therapeutic targeting in immune-related disorders.

Exploring the Multiple Roles of Notch1 in Biological Development: An Analysis and Study Based on Phylogenetics and Transcriptomics

At present, there is a research gap concerning the specific functions and mechanisms of the Notch gene family and its signaling pathway in jawless vertebrates. In this study, we identified a Notch1 homologue (Lr. Notch1) in the Lethenteron reissneri database. Through bioinformatics analysis, we identified Lr. Notch1 as the likely common ancestor gene of the Notch gene family in higher vertebrates, indicating a high degree of conservation in the Notch gene family and its signaling pathways. To validate the biological function of Lr. Notch1, we conducted targeted silencing of Lr. Notch1 in L. reissneri and analyzed the resultant gene expression profile before and after silencing using transcriptome analysis. Our findings revealed that the silencing of Lr. Notch1 resulted in differential expression of pathways and genes associated with signal transduction, immune regulation, and metabolic regulation, mirroring the biological function of the Notch signaling pathway in higher vertebrates. This article systematically elucidated the origin and evolution of the Notch gene family while also validating the biological function of Lr. Notch1. These insights offer valuable clues for understanding the evolution of the Notch signaling pathway and establish a foundation for future research on the origin of the Notch signaling pathway, as well as its implications in human diseases and immunomodulation.

Genomic view of the origins of cell-mediated immunity

NKp30 is an activating natural killer cell receptor (NKR) with a single-exon variable (VJ)-type immunoglobulin superfamily (IgSF) domain. Such VJ-IgSF domains predate the emergence of the antigen receptors (immunoglobulin and T cell receptor), which possess the same domain but undergo gene rearrangement. NCR3, the gene encoding NKp30, is present in jawed vertebrates from sharks to mammals; thus, unlike most NKR that are highly divergent among vertebrate taxa, NKp30 is uniquely conserved. We previously hypothesized that an ancestral NCR3 gene was encoded in the proto-major histocompatibility complex (MHC), the region where many immune-related genes have accumulated. Herein, we searched in silico databases to identify NCR3 paralogues and examined their genomic locations. We found a paralogue, NCR3H, in many vertebrates but was lost in mammals. Additionally, we identified a set of voltage-gated sodium channel beta (SCNB) genes as NCR3-distantly-related genes. Like NCR3, both NCR3H and SCNB proteins contain a single VJ-IgSF domain followed by a transmembrane region. These genes map to MHC paralogous regions, originally described in an invertebrate, along with genes encoding cell adhesion molecules involved in NK cell recognition networks. Other genes having no obvious relationship to immunity also map to these paralogous regions. These gene complexes were traced to several invertebrates, suggesting that the foundation of these cellular networks emerged before the genome-wide duplications in early gnathostome history. Here, we propose that this ancestral region was involved in cell-mediated immunity prior to the emergence of adaptive immunity and that NCR3 piggybacked onto this primordial complex, heralding the emergence of vertebrate NK cell/T cells.

The Dual Role of the Innate Immune System in the Effectiveness of mRNA Therapeutics

Advances in molecular biology have revolutionized the use of messenger RNA (mRNA) as a therapeutic. The concept of nucleic acid therapy with mRNA originated in 1990 when Wolff et al. reported successful expression of proteins in target organs by direct injection of either plasmid DNA or mRNA. It took decades to bring the transfection efficiency of mRNA closer to that of DNA. The next few decades were dedicated to turning in vitro-transcribed (IVT) mRNA from a promising delivery tool for gene therapy into a full-blown therapeutic modality, which changed the biotech market rapidly. Hundreds of clinical trials are currently underway using mRNA for prophylaxis and therapy of infectious diseases and cancers, in regenerative medicine, and genome editing. The potential of IVT mRNA to induce an innate immune response favors its use for vaccination and immunotherapy. Nonetheless, in non-immunotherapy applications, the intrinsic immunostimulatory activity of mRNA directly hinders the desired therapeutic effect since it can seriously impair the target protein expression. Targeting the same innate immune factors can increase the effectiveness of mRNA therapeutics for some indications and decrease it for others, and vice versa. The review aims to present the innate immunity-related 'barriers' or 'springboards' that may affect the development of immunotherapies and non-immunotherapy applications of mRNA medicines.

Mechanisms of interactions in pattern-recognition of common glycostructures across pectin-derived heteropolysaccharides by Toll-like receptor 4

Complex pectin, originating from terrestrial plant cell walls has been attracting research attention as a promising source of a new innate immune modulator. Numerous bioactive polysaccharides associated with pectin are newly reported every year, but the general mechanism of their immunological action remains unclear owing to the complexity and heterogeneity of pectin. Herein, we systematically investigated the interactions in pattern-recognition for common glycostructures of pectic heteropolysaccharides (HPSs) by Toll-like receptors (TLRs). The compositional similarity of glycosyl residues derived from pectic HPS was confirmed by conducting systematic reviews, leading to molecular modeling of representative pectic segments. Via structural investigation, the inner concavity of leucine-rich repeats of TLR4 was predicted to act as a binding motif for carbohydrate recognition, and subsequent simulations predicted the binding modes and conformations. We experimentally demonstrated that pectic HPS exhibits the non-canonical and multivalent binding aspects for TLR4 resulting in receptor activation. Furthermore, we showed that pectic HPSs were selectively clustered with TLR4 during endocytosis, inducing downstream signals to cause phenotypic activation of macrophages. Overall, we have presented a better explanation for the pattern recognition of pectic HPS and further proposed an approach to understand the interaction between complex carbohydrates and proteins.

The adaptive microbiome hypothesis and immune interactions in amphibian mucus

The microbiome is known to provide benefits to hosts, including extension of immune function. Amphibians are a powerful immunological model for examining mucosal defenses because of an accessible epithelial mucosome throughout their developmental trajectory, their responsiveness to experimental treatments, and direct interactions with emerging infectious pathogens. We review amphibian skin mucus components and describe the adaptive microbiome as a novel process of disease resilience where competitive microbial interactions couple with host immune responses to select for functions beneficial to the host. We demonstrate microbiome diversity, specificity of function, and mechanisms for memory characteristic of an adaptive immune response. At a time when industrialization has been linked to losses in microbiota important for host health, applications of microbial therapies such as probiotics may contribute to immunotherapeutics and to conservation efforts for species currently threatened by emerging diseases.

Seascape genomics reveals limited dispersal and suggests spatially varying selection among European populations of sea lamprey (Petromyzon marinus)

Sea lamprey Petromyzon marinus is an anadromous and semelparous fish without homing behaviors. Despite being a freshwater, free-living organism for a large part of their life cycle, its adulthood is spent as a parasite of marine vertebrates. In their native European range, while it is well-established that sea lampreys comprise a single nearly-panmictic population, few studies have further explored the evolutionary history of natural populations. Here, we performed the first genome-wide characterization of sea lamprey's genetic diversity in their European natural range. The objectives were to investigate the connectivity among river basins and explore evolutionary processes mediating dispersal during the marine phase, with the sequencing of 186 individuals from 8 locations spanning the North Eastern Atlantic coast and the North Sea with double-digest RAD-sequencing, obtaining a total of 30,910 bi-allelic SNPs. Population genetic analyses reinforced the existence of a single metapopulation encompassing freshwater spawning sites within the North Eastern Atlantic and the North Sea, though the prevalence of private alleles at northern latitudes suggested some limits to the species' dispersal. Seascape genomics suggested a scenario where oxygen concentration and river runoffs impose spatially varying selection across their distribution range. Exploring associations with the abundance of potential hosts further suggested that hake and cod could also impose selective pressures, although the nature of such putative biotic interactions was unresolved. Overall, the identification of adaptive seascapes in a panmictic anadromous species could contribute to conservation practices by providing information for restoration activities to mitigate local extinctions on freshwater sites.

TULA Proteins in Men, Mice, Hens, and Lice: Welcome to the Family

The two members of the UBASH3/STS/TULA protein family have been shown to critically regulate key biological functions, including immunity and hemostasis, in mammalian biological systems. Negative regulation of signaling through immune receptor tyrosine-based activation motif (ITAM)- and hemITAM-bearing receptors mediated by Syk-family protein tyrosine kinases appears to be a major molecular mechanism of the down-regulatory effect of TULA-family proteins, which possess protein tyrosine phosphatase (PTP) activity. However, these proteins are likely to carry out some PTP-independent functions as well. Whereas the effects of TULA-family proteins overlap, their characteristics and their individual contributions to cellular regulation also demonstrate clearly distinct features. Protein structure, enzymatic activity, molecular mechanisms of regulation, and biological functions of TULA-family proteins are discussed in this review. In particular, the usefulness of the comparative analysis of TULA proteins in various metazoan taxa, for identifying potential roles of TULA-family proteins outside of their functions already established in mammalian systems, is examined.

Review of the unique and dominant lectin pathway of complement activation in agnathans

As the most primitive vertebrates, lampreys are significant in understanding the early origin and evolution of the vertebrate innate and adaptive immune systems. The complement system is a biological response system with complex and precise regulatory mechanisms and plays an important role in innate and adaptive immunity. It consists of more than 30 distinct components, including intrinsic components, regulatory factors, and complement receptors. Complement system is the humoral backbone of the innate immune defense and complement-like factors have also been found in cyclostomes. Our knowledge as such in lamprey has dramatically increased in the recent years. The searching for complement components in the reissner lamprey Lethenteron reissneri genome database, together with published data, has unveiled the existence of all the orthologues of mammalian complement components identified thus far, including the complement regulatory proteins and complement receptors, in lamprey. This review, summarizes the key themes and recent updates on the complement system of agnathans and discusses the individual complement components of lampreys, and critically compare their functions to that of mammalian complement components. Interestingly, the adaptive immune system of agnathans differs from that of gnathostomes. Lamprey complement components also display some distinctive features, such as lampreys are characterized by the variable lymphocyte receptors (VLRs)-based alternative adaptive immunity. This review may serve as important literature for deducing the evolution of the immune system from invertebrates to vertebrates.

Molecular characterization and expression analysis of a novel cold-inducible RNA-binding protein (CIRBP) gene in lamprey (Lethenteron reissneri)

Cold-inducible RNA-binding protein (CIRBP) responds to a wide array of cellular stresses such as cold shock, hypoxia, and inflammatory responses. However, functional studies of CIRBP in jawless vertebrates are limited. In this study, a CIRBP homolog from the jawless vertebrate lamprey (Lethenteron reissneri) was cloned and characterized (named Lr-CIRBP). The cDNA fragment of Lr-CIRBP has a 516 bp open reading frame (ORF) that encodes 171 amino acids, comprising a glycine-rich region at the C-terminal, similar to higher vertebrates but slightly shorter, and an RNA recognition motif (RRM) domain at the N-terminus. The predicted Lr-CIRBP sequence had 51.4 ~ 70.6% similarity with CIRBPs from other vertebrates. Further phylogenetic analysis revealed that Lr-CIRBP is located in the outgroup of vertebrates and is the ancestor of vertebrates. Based on real-time quantitative PCR experimental analysis, Lr-CIRBP expression was highest in leukocytes and increased significantly after multi-stimulation, peaking at 12 h. RNA interference showed that Lr-CIRBP knockdown can down-regulate the expression of inflammatory factors in Lethenteron reissneri. In conclusion, our study successfully clarifies the ancestral features and functions of CIRBP, while revealing valuable insight into how the protein is involved in the immune responses of a jawless vertebrate.

Surfing on the waves of the human γδ T cell ontogenic sea

While γδ T cells are present virtually in all vertebrates, there is a remarkable lack of conservation of the TRG and TRD loci underlying the generation of the γδ T cell receptor (TCR), which is associated with the generation of species-specific γδ T cells. A prominent example is the human phosphoantigen-reactive Vγ9Vδ2 T cell subset that is absent in mice. Murine γδ thymocyte cells were among the first immune cells identified to follow a wave-based layered development during embryonic and early life, and since this initial observation, in-depth insight has been obtained in their thymic ontogeny. By contrast, less is known about the development of human γδ T cells, especially regarding the generation of γδ thymocyte waves. Here, after providing an overview of thymic γδ wave generation in several vertebrate classes, we review the evidence for γδ waves in the human fetal thymus, where single-cell technologies have allowed the breakdown of human γδ thymocytes into functional waves with important TCR associations. Finally, we discuss the possible mechanisms contributing to the generation of waves of γδ thymocytes and their possible significance in the periphery.

Investigation of the Molecular Evolution of Treg Suppression Mechanisms Indicates a Convergent Origin

Regulatory T cell (Treg) suppression of conventional T cells is a central mechanism that ensures immune system homeostasis. The exact time point of Treg emergence is still disputed. Furthermore, the time of Treg-mediated suppression mechanisms’ emergence has not been identified. It is not yet known whether Treg suppression mechanisms diverged from a single pathway or converged from several sources. We investigated the evolutionary history of Treg suppression pathways using various phylogenetic analysis tools. To ensure the conservation of function for investigated proteins, we augmented our study using nonhomology-based methods to predict protein functions among various investigated species and mined the literature for experimental evidence of functional convergence. Our results indicate that a minority of Treg suppressor mechanisms could be homologs of ancient conserved pathways. For example, CD73, an enzymatic pathway known to play an essential role in invertebrates, is highly conserved between invertebrates and vertebrates, with no evidence of positive selection (w = 0.48, p-value < 0.00001). Our findings indicate that Tregs utilize homologs of proteins that diverged in early vertebrates. However, our findings do not exclude the possibility of a more evolutionary pattern following the duplication degeneration−complementation (DDC) model. Ancestral sequence reconstruction showed that Treg suppression mechanism proteins do not belong to one family; rather, their emergence seems to follow a convergent evolutionary pattern.

IL-2-mTORC1 signaling coordinates the STAT1/T-bet axis to ensure Th1 cell differentiation and anti-bacterial immune response in fish

Utilization of specialized Th1 cells to resist intracellular pathogenic infection represents an important innovation of adaptive immunity. Although transcriptional evidence indicates the potential presence of Th1-like cells in some fish species, the existence of CD3+CD4+IFN-γ+ T cells, their detailed functions, and the mechanism determining their differentiation in these early vertebrates remain unclear. In the present study, we identified a population of CD3+CD4-1+IFN-γ+ (Th1) cells in Nile tilapia upon T-cell activation in vitro or Edwardsiella piscicida infection in vivo. By depleting CD4-1+ T cells or blocking IFN-γ, Th1 cells and their produced IFN-γ were found to be essential for tilapia to activate macrophages and resist the E. piscicida infection. Mechanistically, activated T cells of tilapia produce IL-2, which enhances the STAT5 and mTORC1 signaling that in turn trigger the STAT1/T-bet axis-controlled IFN-γ transcription and Th1 cell development. Additionally, mTORC1 regulates the differentiation of these cells by promoting the proliferation of CD3+CD4-1+ T cells. Moreover, IFN-γ binds to its receptors IFNγR1 and IFNγR2 and further initiates a STAT1/T-bet axis-mediated positive feedback loop to stabilize the Th1 cell polarization in tilapia. These findings demonstrate that, prior to the emergence of tetrapods, the bony fish Nile tilapia had already evolved Th1 cells to fight intracellular bacterial infection, and support the notion that IL-2-mTORC1 signaling coordinates the STAT1/T-bet axis to determine Th1 cell fate, which is an ancient mechanism that has been programmed early during vertebrate evolution. Our study is expected to provide novel perspectives into the evolution of adaptive immunity.

Transcriptome-wide analysis of cellular immune response stimulated by nuclear input of different down syndrome cell adhesion molecule intracellular domains

In arthropods, Dscam (Down syndrome cell adhesion molecule) produces multiple pathogen specific receptors via immune responsive alternative splicing, generating molecular complexity analogous to vertebrate antibodies. Fewer isoforms are produced by the exons encoding Dscam's intracellular domain (ICD); therefore, the present study aimed to determine the transcriptional response of Eriocheir sinensis to Dscam ICDs. In the group overexpressing all cytoplasmic tail exons (ICD-FL), 1401 differentially expressed genes (DEGs) were identified; overexpressed of ICD constructs lacking exon-35 (ICD-△35) identified 413 DEGs; and overexpression of ICD constructs lacking exon-35 and exon-36 (ICD-△35 + 36) identified 22 DEGs. The DEGs were enriched in immunity and metabolism-related pathways. The expression of selected genes was confirmed using quantitative real-time reverse transcription PCR. The transcriptomes of Drosophila S2 cells overexpressing different ICDs were then determined. We identified key immune, metabolic, and cell proliferation-regulated genes and gene networks, providing insights into the membrane-to-nuclear signaling pathway of Dscam.

Current knowledge of immune priming in invertebrates, emphasizing studies on Tenebrio molitor

Vertebrates rely on the most sophisticated adaptive immunity to defend themselves against various pathogens. This includes immunologic memory cells, which mount a stronger and more effective immune response against an antigen after its first encounter. Unlike vertebrates, invertebrates' defense completely depends on the innate immunity mechanisms including humoral and cell-mediated immunity. Furthermore, the invertebrate equivalent of the memory cells was discovered only recently. Since the discovery of transgenerational immune priming (TGIP) in crustaceans, numerous findings have proven the IP in invertebrate classes such as insects. TGIP can be induced through maternal priming pathways such as transcriptional regulation of antimicrobial peptides, and also paternal IP including the induction of proPO system activity. We appraise the diversity and specificity of IP agents to provide sustained immunologic memory in insects, particularly T. molitor in the review. An understanding of IP (more so TGIP) response in T. molitor will deepen our knowledge of invertebrate immunity, and boost the mass-rearing industry by reducing pathogen infection rates.

May the Odds Be Ever in Your Favor: Non-deterministic Mechanisms Diversifying Cell Surface Molecule Expression

How does the information in the genome program the functions of the wide variety of cells in the body? While the development of biological organisms appears to follow an explicit set of genomic instructions to generate the same outcome each time, many biological mechanisms harness molecular noise to produce variable outcomes. Non-deterministic variation is frequently observed in the diversification of cell surface molecules that give cells their functional properties, and is observed across eukaryotic clades, from single-celled protozoans to mammals. This is particularly evident in immune systems, where random recombination produces millions of antibodies from only a few genes; in nervous systems, where stochastic mechanisms vary the sensory receptors and synaptic matching molecules produced by different neurons; and in microbial antigenic variation. These systems employ overlapping molecular strategies including allelic exclusion, gene silencing by constitutive heterochromatin, targeted double-strand breaks, and competition for limiting enhancers. Here, we describe and compare five stochastic molecular mechanisms that produce variety in pathogen coat proteins and in the cell surface receptors of animal immune and neuronal cells, with an emphasis on the utility of non-deterministic variation.

Hepatic cecum: a key integrator of immunity in amphioxus

The vertebrate liver is regarded as an organ essential to the regulation of immunity and inflammation as well as being central to the metabolism of nutrients. Here, we discuss the functions that the hepatic cecum of amphioxus plays in the regulation of immunity and inflammation, and the molecular basis of this. It is apparent that the hepatic cecum performs important roles in the immunity of amphioxus including immune surveillance, clearance of pathogens and acute phase response. Therefore, the hepatic cecum, like the vertebrate liver, is an organ functioning as a key integrator of immunity in amphioxus.

Novel lamprey antibody recognizes terminal sulfated galactose epitopes on mammalian glycoproteins

The terminal galactose residues of N- and O-glycans in animal glycoproteins are often sialylated and/or fucosylated, but sulfation, such as 3-O-sulfated galactose (3-O-SGal), represents an additional, but poorly understood modification. To this end, we have developed a novel sea lamprey variable lymphocyte receptor (VLR) termed O6 to explore 3-O-SGal expression. O6 was engineered as a recombinant murine IgG chimera and its specificity and affinity to the 3-O-SGal epitope was defined using a variety of approaches, including glycan and glycoprotein microarray analyses, isothermal calorimetry, ligand-bound crystal structure, FACS, and immunohistochemistry of human tissue macroarrays. 3-O-SGal is expressed on N-glycans of many plasma and tissue glycoproteins, but recognition by O6 is often masked by sialic acid and thus exposed by treatment with neuraminidase. O6 recognizes many human tissues, consistent with expression of the cognate sulfotransferases (GAL3ST-2 and GAL3ST-3). The availability of O6 for exploring 3-O-SGal expression could lead to new biomarkers for disease and aid in understanding the functional roles of terminal modifications of glycans and relationships between terminal sulfation, sialylation and fucosylation.

Proteomic Analysis of the Responses to Co-Stimulation of Intestinal Aeromonas and Shewanella in Lamprey Leukocytes

Lamprey, one of the most basal jawless vertebrate, is an excellent model for studying vertebrate evolution, embryo development, and the origin of adaptive immunity. This study investigated the differentially expressed proteins in lamprey leukocytes in response to the co-stimulation of intestinal Aeromonas and Shewanella by using quantitative proteomics techniques. Significant differentially expressed proteins were identified. Gene Ontology annotation and the Kyoto Encyclopedia of Genes and Genomes pathway based on the significant differentially expressed proteins were analyzed. Most of the differentially expressed proteins were predicted to be involved in important signaling pathways. Quantitative real-time polymerase chain reaction was used to verify the expression of differentially expressed proteins at the mRNA level. The expression of some differentially expressed proteins was not consistent at the mRNA and protein levels. Differentially expressed proteins that are essential for lamprey-intestinal bacteria interaction should be identified to understand the lamprey adaptive immune response induced by gut microbiota.

Immunity against Lagovirus europaeus and the Impact of the Immunological Studies on Vaccination

In the early 1980s, a highly contagious viral hemorrhagic fever in rabbits (Oryctolagus cuniculus) emerged, causing a very high rate of mortality in these animals. Since the initial occurrence of the rabbit hemorrhagic disease virus (RHDV), several hundred million rabbits have died after infection. The emergence of genetically-different virus variants (RHDV GI.1 and GI.2) indicated the very high variability of RHDV. Moreover, with these variants, the host range broadened to hare species (Lepus). The circulation of RHDV genotypes displays different virulences and a limited induction of cross-protective immunity. Interestingly, juvenile rabbits (<9 weeks of age) with an immature immune system display a general resistance to RHDV GI.1, and a limited resistance to RHDV GI.2 strains, whereas less than 3% of adult rabbits survive an infection by either RHDV GI.1. or GI.2. Several not-yet fully understood phenomena characterize the RHD. A very low infection dose followed by an extremely rapid viral replication could be simplified to the induction of a disseminated intravascular coagulopathy (DIC), a severe loss of lymphocytes—especially T-cells—and death within 36 to 72 h post infection. On the other hand, in animals surviving the infection or after vaccination, very high titers of RHDV-neutralizing antibodies were induced. Several studies have been conducted in order to deepen the knowledge about the virus’ genetics, epidemiology, RHDV-induced pathology, and the anti-RHDV immune responses of rabbits in order to understand the phenomenon of the juvenile resistance to this virus. Moreover, several approaches have been used to produce efficient vaccines in order to prevent an infection with RHDV. In this review, we discuss the current knowledge about anti-RHDV resistance and immunity, RHDV vaccination, and the further need to establish rationally-based RHDV vaccines.

IgH 3' regulatory region increases ectopic class switch recombination

DNA lesions inflicted by activation-induced deaminase (AID) instrumentally initiate the processes reshaping immunoglobulin genes in mature B-cells, from local somatic hypermutation (SHM) to junctions of distant breaks during class switch recombination (CSR). It remains incompletely understood how these divergent outcomes of AID attacks are differentially and temporally focused, with CSR strictly occurring in the Ig heavy chain (IgH) locus while SHM concentrates on rearranged V(D)J regions in the IgH and Ig light chain loci. In the IgH locus, disruption of either the 3’Regulatory Region (3’RR) super-enhancer or of switch (S) regions preceding constant genes, profoundly affects CSR. Reciprocally, we now examined if these elements are sufficient to induce CSR in a synthetic locus based on the Igκ locus backbone. Addition of a surrogate “core 3’RR” (c3’RR) and of a pair of transcribed and spliced Switch regions, together with a reporter system for “κ-CSR” yielded a switchable Igκ locus. While the c3’RR stimulated SHM at S regions, it also lowered the local SHM threshold necessary for switch recombination to occur. The 3’RR thus both helps recruit AID to initiate DNA lesions, but then also promotes their resolution through long-distance synapses and recombination following double-strand breaks.

Class switching allows B lymphocytes to replace expression of immunoglobin M with that of immunoglobulins G, A or E. The genetic support of class switching, is a unique and large deletion uniquely occuring within the immunoglobulin heavy chain (IgH) locus. This recombination is triggered after DNA lesions inflicted by the activation-induced deaminase (AID) enzyme. In immunoglobulin light chain loci, AID only stimulates somatic hypermutation. In such a non-IgH locus, we now show that the IgH 3’ superenhancer can promote junctions between distant DNA breaks and ectopic class switch recombination. This study identifies the minimal elements necessary for class-switch recombination to occur instead of hypermutation in a locus targeted by AID, i.e. transcribed (and spliced) target sites for AID in so-called S regions, and the 3’IgH superenhancer which both helps recruit AID for DNA lesions, and helps repair these lesions through distant gene synapsis and recombination.

Determinants of adenine-mutagenesis in diversity-generating retroelements

Diversity-generating retroelements (DGRs) vary protein sequences to the greatest extent known in the natural world. These elements are encoded by constituents of the human microbiome and the microbial ‘dark matter’. Variation occurs through adenine-mutagenesis, in which genetic information in RNA is reverse transcribed faithfully to cDNA for all template bases but adenine. We investigated the determinants of adenine-mutagenesis in the prototypical Bordetella bacteriophage DGR through an in vitro system composed of the reverse transcriptase bRT, Avd protein, and a specific RNA. We found that the catalytic efficiency for correct incorporation during reverse transcription by the bRT-Avd complex was strikingly low for all template bases, with the lowest occurring for adenine. Misincorporation across a template adenine was only somewhat lower in efficiency than correct incorporation. We found that the C6, but not the N1 or C2, purine substituent was a key determinant of adenine-mutagenesis. bRT-Avd was insensitive to the C6 amine of adenine but recognized the C6 carbonyl of guanine. We also identified two bRT amino acids predicted to nonspecifically contact incoming dNTPs, R74 and I181, as promoters of adenine-mutagenesis. Our results suggest that the overall low catalytic efficiency of bRT-Avd is intimately tied to its ability to carry out adenine-mutagenesis.

Gut-derived Shewanella induces the differentially expressed proteins in leukocytes of Lampetra japonica

Lampreys, one of the most basal jawless vertebrates, are an excellent animal model for investigating vertebrate evolution, embryonic development, and the origin of adaptive immunity. Gut-derived Shewanella strain was isolated and then proved to induce adaptive immunity response in lampreys. Using Shewanella as the antigen, the effect of gut-derived Shewanella on lamprey leukocyte proteome was investigated via label-free liquid chromatography-tandem mass spectrometry for quantitative proteomics analysis. Twenty-five differentially expressed proteins in lamprey leukocytes were identified with significant differences. The differentially expressed proteins were associated with several biological processes. Among these proteins, the signal transducer and activator of transcription 3 (STAT3) was significantly upregulated in leukocytes after Shewanella immunization, indicating that lamprey STAT3 (L-STAT3) was involved in Shewanella-lamprey interactions. Expression pattern analysis revealed that L-STAT3 was mainly distributed in the cytoplasm and upregulated in other tissues after Shewanella immunization. Moreover, L-STAT3 overexpression could promote HEK-293 T and HeLa cell proliferation. However, the functions of L-STAT3 in the adaptive immune response of lamprey induced by gut-derived Shewanella remain to be explored. Overall, the identification of leukocyte proteins involved in Shewanella-lamprey interactions provides important information for understanding the variable lymphocyte receptor-based adaptive immune signal pathways in lampreys. SIGNIFICANCE: Lampreys are considered to be an excellent animal model for studying the origin and development of adaptive immune systems in vertebrates. Lampreys use variable lymphocyte receptors (VLRs) in recognizing antigens. However, the understanding of the VLR-based adaptive immune signal pathways in lampreys remains unclear. Intestinal bacteria could regulate the development of host immune systems. The attempts of inducing lamprey leukocyte differentially expressed proteins using the gut bacterial as the antigen will supply an promising avenue to explore the molecular mechanism of the intestinal bacteria interaction with it's host. Also, the identification of differentially expressed proteins involved in interactions between gut-derived Shewanella and lamprey will supply clues for understanding the variable lymphocyte receptor-based adaptive immune signal pathways in lampreys.

The thymus and the science of self

The conventional perception asserts that immunology is the science of ‘discrimination’ between self and non-self. This concept is however no longer tenable as effector cells of the adaptive immune system are first conditioned to be tolerant to the body’s own antigens, collectively known as self until now. Only then attain these effectors the responsiveness to non-self. The acquisition of this essential state of tolerance to self occurs for T cells in the thymus, the last major organ of our body that revealed its intricate function in health and disease. The ‘thymus’ as an anatomical notion was first notably documented in Ancient Greece although our present understanding of the organ’s functions was only deciphered commencing in the 1960s. In the late 1980s, the thymus was identified as the site where clones of cells reactive to self, termed ‘forbidden’ thymocytes, are physically depleted as the result of a process now known as negative selection. The recognition of this mechanism further contributed to the belief that the central rationale of immunology as a science lies in the distinction between self and non-self. This review will discuss the evidence that the thymus serves as a unique lymphoid organ able to instruct T cells to recognize and be tolerant to harmless self before adopting the capacity to defend the body against potentially injurious non-self-antigens presented in the context of different challenges from infections to exposure to malignant cells. The emerging insight into the thymus’ cardinal functions now also provides an opportunity to exploit this knowledge to develop novel strategies that specifically prevent or even treat organ-specific autoimmune diseases.

Natural Killer T Lymphocytes Integrate Innate Sensory Information and Relay Context to Effector Immune Responses

It is now appreciated that a group of lymphoid lineage cells, collectively called innate-like effector lymphocytes, have evolved to integrate information relayed by the innate sensory immune system about the state of the local tissue environment and to pass on this context to downstream effector innate and adaptive immune responses. Thereby, innate functions engrained into such innate-like lymphoid lineage cells during development can control the quality and magnitude of an immune response to a tissue-altering pathogen and facilitate the formation of memory engrams within the immune system. These goals are accomplished by the innate lymphoid cells that lack antigen-specific receptors, γδ T cell receptor (TCR)-expressing T cells, and several αβ TCR-expressing T cell subsets-such as natural killer T cells, mucosal-associated invariant T cells, et cetera. Whilst we briefly consider the commonalities in the origins and functions of these diverse lymphoid subsets to provide context, the primary topic of this review is to discuss how the semi-invariant natural killer T cells got this way in evolution through lineage commitment and onward ontogeny. What emerges from this discourse is the question: Has a "limbic immune system" emerged (screaming quietly in plain sight!) out of what has been dubbed "in-betweeners"?

Structural biology of plant defence

Plants employ the innate immune system to discriminate between self and invaders through two types of immune receptors, one on the plasma membrane and the other in the intracellular space. The immune receptors on the plasma membrane are pattern recognition receptors (PRRs) that can perceive pathogen-associated molecular patterns (PAMPs) or host-derived damage-associated molecular patterns (DAMPs) leading to pattern-triggered immunity (PTI). Particular pathogens are capable of overcoming PTI by secreting specific effectors into plant cells to perturb different components of PTI signalling through various mechanisms. Most of the immune receptors from the intracellular space are the nucleotide-binding leucine-rich repeat receptors (NLRs), which specifically recognize pathogen-secreted effectors to mediate effector-triggered immunity (ETI). In this review, we will summarize recent progress in structural studies of PRRs, NLRs, and effectors, and discuss how these studies shed light on ligand recognition and activation mechanisms of the two types of immune receptors and the diversified mechanisms used by effectors to manipulate plant immune signalling.

The immune system of jawless vertebrates: insights into the prototype of the adaptive immune system

Jawless vertebrates diverged from an ancestor of jawed vertebrates approximately 550 million years ago. They mount adaptive immune responses to repetitive antigenic challenges, despite lacking major histocompatibility complex molecules, immunoglobulins, T cell receptors, and recombination-activating genes. Instead of B cell and T cell receptors, agnathan lymphocytes express unique antigen receptors named variable lymphocyte receptors (VLRs), which generate diversity through a gene conversion-like mechanism. Although gnathostome antigen receptors and VLRs are structurally unrelated, jawed and jawless vertebrates share essential features of lymphocyte-based adaptive immunity, including the expression of a single type of receptor on each lymphocyte, clonal expansion of antigen-stimulated lymphocytes, and the dichotomy of cellular and humoral immunity, indicating that the backbone of the adaptive immune system was established in a common ancestor of all vertebrates. Furthermore, recent evidence indicates that, unlike previously thought, agnathans have a unique classical pathway of complement activation where VLRB molecules act as antibodies instead of immunoglobulins. It seems likely that the last common ancestor of all vertebrates had an adaptive immune system resembling that of jawless vertebrates, suggesting that, as opposed to jawed vertebrates, agnathans have retained the prototype of vertebrate adaptive immunity.

Enhanced Immune Protection of Mud Crab Scylla paramamosain in Response to the Secondary Challenge by Vibrio parahaemolyticus

“Immune priming” plays a vital part in the immune system of invertebrates, protecting against recurrent infections by pathogens, and can provide some ideas for the prevention and treatment of invertebrate diseases. Many invertebrates have been demonstrated recently to have immune priming, but the relevant mechanisms are not known. Expression of immune system–related genes in the hemocytes and hepatopancreas of the mud crab (Scylla paramamosain) before and after repeated stimulation with Vibrio parahaemolyticus were analyzed by real-time fluorescence quantitative polymerase chain reaction. Some molecules that may participate in the immune priming of S. paramamosain were screened out, and their possible roles in immune priming were interpreted. Crabs injected first with heat-killed V. parahaemolyticus (HkVp group) or physiologic (0.9%) saline (PS group) were rechallenged at 168 h with live V. parahaemolyticus (HkVp+Vp group and PS+Vp group, respectively). The log-rank test shows a significant difference in survival rate between the HkVp+Vp group and the other groups after the ICH (p < 0.05). Expression of genes involved in the toll-like receptor (TLR) signaling pathway and some antimicrobial peptide genes were detected. By, respectively, comparing gene quantification at different time points in hemocytes and the hepatopancreas, the molecules that may play a part in the early stage of the immune priming of S. paramamosain in the hemocytes are found to be down syndrome cell adhesion molecule (Dscam), Hyastatin, Cactus, Arasin, antilipopolysaccharide factor 3 (ALF3), ALF4, ALF5, and ALF6 as well as later acting molecules, such as Crustin, Dorsal, Pelle, and myeloid differentiation factor 88 (MyD88). The molecules that functioned throughout the entire period are TLR and Spaetzle. In the hepatopancreas, the molecules that may play a part in the early stages of immune priming are Dscam, Hyastatin, Arasin, ALF6, Pelle, Spaetzle, Dorsal and, in the later stage, ALF4. The molecules that functioned throughout the entire period are TLR, Crustin, Cactus, MyD88, ALF3, and ALF5. In summary, the immune function of S. paramamosain is enhanced after it receives the same repetitive stimulation by V. parahaemolyticus, indicating immune priming in S. paramamosain. Our study enriches research on immune priming in invertebrates and lays the foundation for further studies revealing the molecular mechanism of immune priming in crabs.

Computational Identification of Repeat-Containing Proteins and Systems

Repetitive sequence elements in proteins and nucleic acids are often signatures of adaptive or reprogrammable systems in nature. Known examples of these systems, such as transcriptional activator-like effectors (TALE) and CRISPR, have been harnessed as powerful molecular tools with a wide range of applications including genome editing. The continued expansion of genomic sequence databases raises the possibility of prospectively identifying new such systems by computational mining. By leveraging sequence repeats as an organizing principle, here we develop a systematic genome mining approach to explore new types of naturally adaptive systems, five of which are discussed in greater detail. These results highlight the existence of a diverse range of intriguing systems in nature that remain to be explored and also provide a framework for future discovery efforts.

Lamprey VLRB participates in pathogen detection, VLRB/L-BLNK/L-NF-κB (B-like cells) signal transduction, and development

In jawed vertebrates, B cell receptors (BCR) are primary pathogen detectors that activate downstream signaling pathways to express adaptive immune effectors. In jawless vertebrates, the variable lymphocyte receptors (VLR) B positive lymphocytes can express and secrete specific VLRB molecules in an analogous manner to that of immunoglobulins by B cells in jawed vertebrates. Our study is the first to demonstrate the possibility of incubation of fertilized eggs and artificial breeding of Lampetra morii larvae throughout their life cycle under laboratory condition. We also found that VLRB, lamprey B-cell linker (L-BLNK), and lamprey nuclear factor-kappa B (L-NF-κB) play key roles in early larval development. Aeromonas hydrophila was found to be a lethal pathogen of L. morii larvae causing rapid infection at a concentration of 10⁷ cfu/mL qRT-PCR results revealed that gene expression levels of VLRB, L-BLNK, and L-NF-κB were up-regulated significantly. Ten-day infection trials showed that VLRB, L-BLNK, and L-NF-κB are crucial for lamprey immune response. Furthermore, the expression levels of L-BLNK and L-NF-κB were down-regulated drastically both at mRNA and protein levels after bacterial infection than in the naive group of VLRB morphants. A similar expression pattern of VLRB and L-BLNK was found in L-NF-κB morphants post bacterial infection. The results were strikingly different in the other two morphants. The VLRB and L-NF-κB expression levels were found to be down-regulated at mRNA and protein levels by less than 30% and 45%, respectively, in L-BLNK morphants compared to those in the naive group. These results indicate that L-BLNK and L-NF-κB might participate in VLRB-mediated immune response. Additionally, in VLRB morphants, the mRNA expression levels of some genes, especially the ones expressed in VLRB⁺ lymphocytes but not in VLRA⁺ lymphocytes, were found to be affected. Therefore, these findings of B-like lymphocytes in lamprey offer key evidence with regard to the evolution of adaptive immunity.

Microbiota-host interactions shape ageing dynamics

Occupying the interface between host and environment, host-associated microbes play fundamental roles in nutrient absorption, essential metabolite synthesis, development of the immune system, defence against pathogens and pathogenesis. Microbiota composition and function is rather stable during adulthood, while it dramatically changes during early development, frailty and disease. Ageing is associated with progressive decrease of homeostasis, often resulting in disruption of the physiological balance between host and commensal microbes, ultimately leading to dysbiosis and host demise. Generally, high microbial diversity is associated with health and a youthful state, while low individual microbial diversity and larger inter-individual microbial diversity is associated with ageing and disease states. Different species are equipped with species-specific commensal, symbiotic and pathogenic microbial communities. How and whether the specific host-microbiota consortia co-evolved with host physiology to ensure homeostasis and promote individual fitness remains an open question. In this essay, we propose that the evolution of vertebrate-specific immune adaptations may have enabled the establishment of highly diverse, species-specific commensal microbial communities. We discuss how the maintenance of intact immune surveillance mechanisms, which allow discrimination between commensal and pathogenic bacteria, fail during ageing and lead to the onset of known ageing-related diseases. We discuss how host-microbiota interactions are key to maintaining homeostasis despite external perturbations, but also how they affect a range of host-specific ageing-related phenotypes. This article is part of the theme issue 'The role of the microbiome in host evolution'.

A glance over the fence: Using phylogeny and species comparison for a better understanding of antigen recognition by human γδ T-cells

Both, jawless and jawed vertebrates possess three lymphocyte lineages defined by highly diverse antigen receptors: Two T-cell- and one B-cell-like lineage. In both phylogenetic groups, the theoretically possible number of individual antigen receptor specificities can even outnumber that of lymphocytes of a whole organism. Despite fundamental differences in structure and genetics of these antigen receptors, convergent evolution led to functional similarities between the lineages. Jawed vertebrates possess αβ and γδ T-cells defined by eponymous αβ and γδ T-cell antigen receptors (TCRs). "Conventional" αβ T-cells recognize complexes of Major Histocompatibility Complex (MHC) class I and II molecules and peptides. Non-conventional T-cells, which can be αβ or γδ T-cells, recognize a large variety of ligands and differ strongly in phenotype and function between species and within an organism. This review describes similarities and differences of non-conventional T-cells of various species and discusses ligands and functions of their TCRs. A special focus is laid on Vγ9Vδ2 T-cells whose TCRs act as sensors for phosphorylated isoprenoid metabolites, so-called phosphoantigens (PAg), associated with microbial infections or altered host metabolism in cancer or after drug treatment. We discuss the role of butyrophilin (BTN)3A and BTN2A1 in PAg-sensing and how species comparison can help in a better understanding of this human Vγ9Vδ2 T-cell subset.

Cognitive and Memory Functions in Plant Immunity

From the time of Thucydides in the 5th century BC, it has been known that specific recognition of pathogens and memory formation are critical components of immune functions. In contrast to the immune system of jawed vertebrates, such as humans and mice, plants lack a circulatory system with mobile immune cells and a repertoire of clonally distributed antigen receptors with almost unlimited specificities. However, without these systems and mechanisms, plants can live and survive in the same hostile environment faced by other organisms. In fact, they achieve specific pathogen recognition and elimination, with limited self-reactivity, and generate immunological memory, sometimes with transgenerational characteristics. Thus, the plant immune system satisfies minimal conditions for constituting an immune system, namely, the recognition of signals in the milieu, integration of that information, subsequent efficient reaction based on the integrated information, and memorization of the experience. In the previous report, this set of elements was proposed as an example of minimal cognitive functions. In this essay, I will first review current understanding of plant immunity and then discuss the unique features of cognitive activities, including recognition of signals from external as well as internal environments, autoimmunity, and memory formation. In doing so, I hope to reach a deeper understanding of the significance of immunity omnipresent in the realm of living organisms.

The evolving role of T-bet in resistance to infection

The identification of T-bet as a key transcription factor associated with the development of IFNγ-producing CD4⁺ T cells predicted a crucial role for T-bet in cell-mediated immunity and in resistance to many intracellular infections. This idea was reinforced by initial reports showing that T-bet-deficient mice were more susceptible to pathogens that survived within the lysosomal system of macrophages. However, subsequent studies revealed IFNγ-dependent, T-bet-independent pathways of resistance to diverse classes of microorganisms that occupy other intracellular niches. Consequently, a more complex picture has emerged of how T-bet and the related transcription factor eomesodermin (EOMES) coordinate many facets of the immune response to bona fide pathogens as well as commensals. This article provides an overview of the discovery and evolutionary relationship between T-bet and EOMES and highlights the studies that have uncovered broader functions of T-bet in innate and adaptive immunity and in the development of the effector and memory T cell populations that mediate long-term resistance to infection.

Identification, functional characterization and the potential role of variable lymphocyte receptor EsVLRA from Eriocheir sinensis in response to secondary challenge after Vibrio parahaemolyticus vaccine

Variable lymphocyte receptors (VLRs) play an important role via their antigen-special reorganization in jawless vertebrates (agnathans) adaptive immune response. In the present study, the open reading frame (ORF) of Eriocheir sinensis VLRA (designated as EsVLRA) was identified. EsVLRA comprised a 799-amino-acid polypeptide with one LRR_NT domain, thirteen LRR domains and one LRR_CT domain, which showed a high domain consistency of the VLR genes in lamprey (Petromyzon marinus). The transcript of EsVLRA was detected in all examined tissues with the highest level detected in hepatopancreas. Notably, the expression of EsVLRA in hepatopancreas, gonads, gill and intestine of male crabs was significantly higher than that in females. The recombinant EsVLRA exhibited strong bacteria-binding activity rather than antibacterial activity, suggesting its crucial role in immune recognition. Furthermore, 6 h earlier response and a significantly higher peak of EsVLRA mRNA expression was observed after challenge with live Vibrio parahaemolyticus (240.6-fold, P < 0.01, crabs receive secondary challenge after V. parahaemolyticus vaccine to the carbs only receive twice PBS injection, N = 6), compared with those only received first injection with formalin-inactivated V. parahaemolyticus (39.7-fold, P < 0.01, challenge 6 h to vaccination 12 h). The findings of this study together demonstrated that EsVLRA plays an important role in the immune system of E. sinensis, serving as a pattern recognition receptor and involving in the immune priming.

A novel complement factor I involving in the complement system immune response from Lampetra morii

Complement factor I (CFI) is a serine protease which plays a key role in the modulation of complement system and the induced-fit factor responsible for controlling the complement-mediated processes. In this study, a CFI gene was cloned and characterized from Lampetra morii (designated as L-CFI) at molecular and cellular levels. The L-CFI protein included a factor I membrane attack complex domain (FIMAC), a scavenger receptor cysteine-rich domain (SRCR), a trypsin-like serine protease domain (Tryp_SPc) and 2 low-density lipoprotein receptor class A domains (LDLa) which would exhibit functional similarities to CFI superfamily proteins. Tissue expression profile analysis showed that L-CFI mRNA constitutively expressed in all tested tissues except erythrocytes, with the predominant expression in liver. The mRNA expression level of L-CFI increased significantly after Vibrio anguillarum and Staphylocccus aureus stimulation. It is demonstrated that L-CFI interacted with L-C3 protein and affected the deposition of L-C3 on the cell surface. Furthermore, lamprey serum after deplete L-CFI and L-C3 reduced the cytotoxic activity against HeLa cells. These findings suggest that L-CFI plays an important role in lamprey immunity and involved in the lamprey complement system.

Engineering repeat proteins of the immune system

Limitations associated with immunoglobulins have motivated the search for novel binding scaffolds. Repeat proteins have emerged as one promising class of scaffolds, but often are limited to binding protein and peptide targets. An exception is the repeat proteins of the immune system, which have in recent years served as an inspiration for binding scaffolds which can bind glycans and other classes of biomolecule. Like other repeat proteins, these proteins can be very stable and have a monomeric mode of binding, with elongated and highly variable binding surfaces. The ability to target glycans and glycoproteins fill an important gap in current tools for research and biomedical applications.

The involvement of TLR signaling and anti-bacterial effectors in enhanced immune protection of oysters after Vibrio splendidus pre-exposure

The phenomena of enhanced protection of innate immunity responding to a pre-exposed pathogen have been reported in invertebrates. The underpinning molecular basis and mechanism for the enhanced immune protection are still missing. In order to explore the possible molecular basis for enhanced immune protection in molluscs, the transcriptomic analysis of oysters Crassostrea gigas hemocytes after twice stimulation of Vibrio splendidus were conducted, and a total of 403 M clean reads and 34254 differentially expressed genes (DEGs) were collected. There were 2964 common DEGs up-regulated in hemocytes after both the first and second immune stimulation, which were mostly enriched in metabolic processes and immune related pathways, such as endocytosis, MAPK signaling pathway and TLR signal pathway. Moreover, 187 and 55 DEGs were higher expressed at resting (0 h after stimulation) and activating state (12 h after stimulation) of the second immune response than that of the first response, respectively, mainly including immune recognition receptor scavenger receptor 2, signal molecule MAPK2, immune regulator IL17-d, apoptosis inhibitor IAP and effector cathepsin. More importantly, 13 DEGs were long-lastingly higher expressed at both the resting and activating state within the second immune response than that of the first, including TLR signal molecule MyD88, anti-virulent tissue inhibitor of metalloproteinase, anti-bacterial proline-rich transmembrane protein, which might play indispensable roles in enhanced immune protection against V. splendidus re-infection. The expression patterns of TLR signals (CgTLR6 and CgMyD88) and effector molecules (CgTIMP and CgPRTP) were further validated by RT-PCR, which were consistent to transcriptomic results. All the results provided an overall molecular basis of enhanced immune protection for hemocytes defensing against the second stimulation of V. splendidus in oyster, which would be valuable for understanding the protection mechanisms of pre-exposure in invertebrates.

A self-marker-like protein governs hemocyte allorecognition in Halocynthia roretzi

BACKGROUND

Self-incompatibility, fusion/non-fusion reactions, and contact reactions (CRs) have all been identified as allorecognition phenomena in ascidians. CR is a reaction characteristic of the hemocytes of Halocynthia roretzi, whereby they release phenol oxidase (PO) upon contact with non-self hemocytes. Thus, these cells may represent a primitive form of the vertebrate immune system. In the present study, we focused on the CR of H. roretzi hemocytes and sought to identify self-marker proteins that distinguish between self and non-self cells.

RESULTS

We initially generated a CR-inducing monoclonal antibody against the complete hemocyte membrane-protein complement (mAb11B16B10). This antibody was identified based on the differential induction of PO activity in individual organisms. The level of PO activity induced by this antibody in individual ascidians was consistent with the observed CR-induced PO activity. mAb11B16B10 recognized a series of 12 spots corresponding to a 100-kDa protein, with differing isoelectric points (pIs). A comparison of the 2D electrophoresis gels of samples from CR-reactive/non-reactive individuals revealed that some spots in this series in hemocytes were common to the CR-non-inducible individuals, but not to CR-inducible individuals. We cloned the corresponding gene and named it Halocynthia roretzi self-marker-like protein-1 (HrSMLP1). This gene is similar to the glycoprotein DD3-3 found in Dictyostelium, and is conserved in invertebrates.

CONCLUSION

We generated a CR-inducing monoclonal antibody (mAb11B16B10) that recognized a series of novel membrane proteins (HrSMLP1) in the hemocytes of H. roretzi. The combination of expressed spots of HrSMLP1 distinguishes non-self cells from self cells with respect to CR inducibility. Given that the HrSMLP1 gene is a single gene, it may represent a novel type of self-marker protein with a role in CR.