A gene family of putative immune recognition molecules in the hydroid Hydractinia

Tissue distribution and expression dynamics of trefoil factor genes in the hydroid Hydractinia symbiolongicarpus

Proteins of the trefoil factor family (TFF) participate in mucosal repair and are formed by single or tandemly repeated trefoil domains. TFFs have been extensively studied in mammals and amphibians, but they have not been functionally characterized in other animals. Here we report the identification of two genes expressed in the hydroid Hydractinia symbiolongicarpus, predicted to encode trefoil domain-containing peptides, one with four trefoil domains in tandem and the other one with a trefoil domain flanked by two ShKT domains. Differential expression analyses by qPCR after an immune challenge and an induced mechanical damage, reveal that the former gene (hysyTFF) had no significant changes in expression after the inductions. However, the latter (hysyTFF-like) was overexpressed after three hours post immune challenge and was downregulated after the first hour post epithelial damage. Immunoblot analyses using specific IgY antibodies revealed that hysyTFF is secreted as a high molecular weight complex. Finally, whole mount immunofluorescence assays showed that hysyTFF was predominantly expressed in the endoderm of stolons and polyps, and sparsely in the ectoderm of both polyps and larvae. Thus, the tissue distribution and expression dynamics of trefoil factor genes in H. symbiolongicarpus suggest that hysyTFF is part of an ancient mechanism of epithelial restitution, and the newly reported hysyTFF-like might act as an immune effector gene, perhaps encoding an antibacterial peptide.

Full-Length Transcriptome Sequencing of the Scleractinian Coral Montipora foliosa Reveals the Gene Expression Profile of Coral-Zooxanthellae Holobiont

Coral-zooxanthellae holobionts are one of the most productive ecosystems in the ocean. With global warming and ocean acidification, coral ecosystems are facing unprecedented challenges. To save the coral ecosystems, we need to understand the symbiosis of coral-zooxanthellae. Although some Scleractinia (stony corals) transcriptomes have been sequenced, the reliable full-length transcriptome is still lacking due to the short-read length of second-generation sequencing and the uncertainty of the assembly results. Herein, PacBio Sequel II sequencing technology polished with the Illumina RNA-seq platform was used to obtain relatively complete scleractinian coral M. foliosa transcriptome data and to quantify M. foliosa gene expression. A total of 38,365 consensus sequences and 20,751 unique genes were identified. Seven databases were used for the gene function annotation, and 19,972 genes were annotated in at least one database. We found 131 zooxanthellae transcripts and 18,829 M. foliosa transcripts. A total of 6328 lncRNAs, 847 M. foliosa transcription factors (TFs), and 2 zooxanthellae TF were identified. In zooxanthellae we found pathways related to symbiosis, such as photosynthesis and nitrogen metabolism. Pathways related to symbiosis in M. foliosa include oxidative phosphorylation and nitrogen metabolism, etc. We summarized the isoforms and expression level of the symbiont recognition genes. Among the membrane proteins, we found three pathways of glycan biosynthesis, which may be involved in the organic matter storage and monosaccharide stabilization in M. foliosa. Our results provide better material for studying coral symbiosis.

The Hydractinia allorecognition system

Hydractinia symbiolongicarpus is a colonial hydroid and a long-standing model system for the study of invertebrate allorecognition. The Hydractinia allorecognition system allows colonies to discriminate between their own tissues and those of unrelated conspecifics that co-occur with them on the same substrate. This recognition mediates spatial competition and mitigates the risk of stem cell parasitism. Here, I review how we have come to our current understanding of the molecular basis of allorecognition in Hydractinia. To date, two allodeterminants have been identified, called Allorecognition 1 (Alr1) and Allorecognition 2 (Alr2), which occupy a genomic region called the allorecognition complex (ARC). Both genes encode highly polymorphic cell surface proteins that are capable of homophilic binding, which is thought to be the mechanism of self/non-self discrimination. Here, I review how we have come to our current understanding of Alr1 and Alr2. Although both are members of the immunoglobulin superfamily, their evolutionary origins remain unknown. Moreover, existing data suggest that the ARC may be home to a family of Alr-like genes, and I speculate on their potential functions.

Innate immunity and cnidarian-Symbiodiniaceae mutualism

The phylum Cnidaria (sea anemones, corals, hydra, jellyfish) is one the most distantly related animal phyla to humans, and yet cnidarians harbor many of the same cellular pathways involved in innate immunity in mammals. In addition to its role in pathogen recognition, the innate immune system has a role in managing beneficial microbes and supporting mutualistic microbial symbioses. Some corals and sea anemones undergo mutualistic symbioses with photosynthetic algae in the family Symbiodiniaceae. These symbioses can be disrupted by anthropogenic disturbances of ocean environments, which can have devastating consequences for the health of coral reef ecosystems. Several studies of cnidarian-Symbiodiniaceae symbiosis have implicated proteins in the host immune system as playing a role in both symbiont tolerance and loss of symbiosis (i.e., bleaching). In this review, we critically evaluate current knowledge about the role of host immunity in the regulation of symbiosis in cnidarians.

The putative immune recognition repertoire of the model cnidarian Hydractinia symbiolongicarpus is large and diverse

Immune recognition of molecular patterns from microorganisms or self-altered cells activate effector responses that neutralize and eliminate these potentially harmful agents. In virtually every metazoan group the process is carried out by pattern recognition receptors, typically constituted by immunoglobulin (Ig), leucine rich repeat (LRR), and/or lectin domains. In order to get insights into the ancestral immune recognition repertoire of animals, we have sequenced the transcriptome of bacterially challenged colonies of the model cnidarian Hydractinia symbiolongicarpus using the Illumina platform. Over 116,000 assembled contigs were annotated by sequence similarity, domain architecture, and functionally. From these, a subset of 315 unique transcripts was predicted as the putative immune recognition repertoire of H. symbiolongicarpus. Interestingly, canonical Toll-like receptors (TLR) were not predicted, nor any transmembrane protein with the Toll/interleukine-1 receptor (TIR) domain. Yet, a variety of predicted proteins with transmembrane domains associated with LRR ectodomains were identified, as well as homologs of the key transduction factor NF-kB, and its associated regulatory proteins. This also has been documented in Hydra, and suggests that recognition and signaling initiation has been decoupled in the TLR system of hydrozoans. In contrast, both canonical and non-canonical NOD-like receptors were identified in H. symbiolongicarpus, showing a higher diversity than the TLR system and perhaps a wider functional landscape. The collection of Ig-like containing putative immune recognition molecules was diverse, and included at least 26 unique membrane-bound predicted proteins and 88 cytoplasmic/secreted predicted molecules. In addition, 25 and 5 transcripts encoding the Ig-like containing allorecognition determinants ALR1 and ALR2, respectively, were identified. Sequence and phylogenetic analyses suggested the presence of various transcriptionally active alr loci, and the action of recombination-based mechanisms diversifying them. Transcripts encoding at least six lectin families with putative roles in immune recognition were found, including 19 unique C-type lectins and 21 unique rhamnose-binding lectins. Other predicted immune recognition receptors included scavenger receptors from three families, lipopolysaccharide-binding proteins, cell-adhesion molecules and thioester-bond containing proteins. This analysis demonstrated that the putative immune recognition repertoire of H. symbiolongicarpus is large and diverse.

A diverse host thrombospondin-type-1 repeat protein repertoire promotes symbiont colonization during establishment of cnidarian-dinoflagellate symbiosis

The mutualistic endosymbiosis between cnidarians and dinoflagellates is mediated by complex inter-partner signaling events, where the host cnidarian innate immune system plays a crucial role in recognition and regulation of symbionts. To date, little is known about the diversity of thrombospondin-type-1 repeat (TSR) domain proteins in basal metazoans or their potential role in regulation of cnidarian-dinoflagellate mutualisms. We reveal a large and diverse repertoire of TSR proteins in seven anthozoan species, and show that in the model sea anemone Aiptasia pallida the TSR domain promotes colonization of the host by the symbiotic dinoflagellate Symbiodinium minutum. Blocking TSR domains led to decreased colonization success, while adding exogenous TSRs resulted in a ‘super colonization’. Furthermore, gene expression of TSR proteins was highest at early time-points during symbiosis establishment. Our work characterizes the diversity of cnidarian TSR proteins and provides evidence that these proteins play an important role in the establishment of cnidarian-dinoflagellate symbiosis.

DOI:http://dx.doi.org/10.7554/eLife.24494.001

Cnidarians, such as corals and sea anemones, often form a close relationship with microscopic algae that live inside their cells – a partnership, on which the entire coral reef ecosystem depends. These microalgae produce sugars and other compounds that the cnidarians need to survive, while the cnidarians protect the microalgae from the environment and provide the raw materials they need to harness energy from sunlight. However, very little is known about how the two partners are able to communicate with each other to form this close relationship, which is referred to as a symbiosis.

Symbiotic relationships between a host and a microbe require a number of adaptations on both sides, and involve numerous signalling molecules. A host species is under constant pressure to develop mechanisms to recognize and tolerate the beneficial microbes without leaving itself vulnerable to attack by microbes that might cause disease. Similarly, the beneficial microbes need to be able to invade and survive inside their host.

Previous research has shown that TSR proteins in hosts play a role in recognizing and controlling disease-causing microbes. Until now, however, it was unknown whether TSR proteins are involved in establishing a symbiosis between cnidarians and their algal partners.

Neubauer et al. analysed six species of symbiotic cnidarians and discovered a diverse repertoire of TSR proteins. These proteins were found in the host genomes, rather than in the symbiotic algae, strongly suggesting that they originated from the host.

Neubauer et al. next incubated a sea anemone species in a solution of TSR proteins and saw that it became ‘super-colonized’ with algae, meaning that over time, millions of the microalgae entered and stayed in the anemone’s tentacles. In contrast, when the TSR proteins were blocked, colonization was almost entirely stopped. This suggests that host TSR proteins play an important role for the microalgae when they colonialize corals and other cnidarians.

The signals that enable microalgae to successfully colonialize cnidarians are unquestionably complex and there is still much to learn. These findings add another piece to the puzzle of how symbiotic algae bypass the cnidarian’s immune system to persist and flourish in their host. An important next step will be to test how blocking the genes that encode the TSR proteins will affect the symbiotic relationship between these species.

DOI:http://dx.doi.org/10.7554/eLife.24494.002

The scavenger receptor repertoire in six cnidarian species and its putative role in cnidarian-dinoflagellate symbiosis

Many cnidarians engage in a mutualism with endosymbiotic photosynthetic dinoflagellates that forms the basis of the coral reef ecosystem. Interpartner interaction and regulation includes involvement of the host innate immune system. Basal metazoans, including cnidarians have diverse and complex innate immune repertoires that are just beginning to be described. Scavenger receptors (SR) are a diverse superfamily of innate immunity genes that recognize a broad array of microbial ligands and participate in phagocytosis of invading microbes. The superfamily includes subclades named SR-A through SR-I that are categorized based on the arrangement of sequence domains including the scavenger receptor cysteine rich (SRCR), the C-type lectin (CTLD) and the CD36 domains. Previous functional and gene expression studies on cnidarian-dinoflagellate symbiosis have implicated SR-like proteins in interpartner communication and regulation. In this study, we characterized the SR repertoire from a combination of genomic and transcriptomic resources from six cnidarian species in the Class Anthozoa. We combined these bioinformatic analyses with functional experiments using the SR inhibitor fucoidan to explore a role for SRs in cnidarian symbiosis and immunity. Bioinformatic searches revealed a large diversity of SR-like genes that resembled SR-As, SR-Bs, SR-Es and SR-Is. SRCRs, CTLDs and CD36 domains were identified in multiple sequences in combinations that were highly homologous to vertebrate SRs as well as in proteins with novel domain combinations. Phylogenetic analyses of CD36 domains of the SR-B-like sequences from a diversity of metazoans grouped cnidarian with bilaterian sequences separate from other basal metazoans. All cnidarian sequences grouped together with moderate support in a subclade separately from bilaterian sequences. Functional experiments were carried out on the sea anemone Aiptasia pallida that engages in a symbiosis with Symbiodinium minutum (clade B1). Experimental blocking of the SR ligand binding site with the inhibitor fucoidan reduced the ability of S. minutum to colonize A. pallida suggesting that host SRs play a role in host-symbiont recognition. In addition, incubation of symbiotic anemones with fucoidan elicited an immune response, indicating that host SRs function in immune modulation that results in host tolerance of the symbionts.

Associations between transcriptional changes and protein phenotypes provide insights into immune regulation in corals

Disease outbreaks in marine ecosystems have driven worldwide declines of numerous taxa, including corals. Some corals, such as Orbicella faveolata, are particularly susceptible to disease. To explore the mechanisms contributing to susceptibility, colonies of O. faveolata were exposed to immune challenge with lipopolysaccharides. RNA sequencing and protein activity assays were used to characterize the response of corals to immune challenge. Differential expression analyses identified 17 immune-related transcripts that varied in expression post-immune challenge. Network analyses revealed several groups of transcripts correlated to immune protein activity. Several transcripts, which were annotated as positive regulators of immunity were included in these groups, and some were downregulated following immune challenge. Correlations between expression of these transcripts and protein activity results further supported the role of these transcripts in positive regulation of immunity. The observed pattern of gene expression and protein activity may elucidate the processes contributing to the disease susceptibility of species like O. faveolata.

Thrombospondin Type-1 Repeat Domain-Containing Proteins Are Strongly Expressed in the Head Region of Hydra

The head region of Hydra, the hypostome, is a key body part for developmental control and the nervous system. We herein examined genes specifically expressed in the head region of Hydra oligactis using suppression subtractive hybridization (SSH) cloning. A total of 1414 subtracted clones were sequenced and found to be derived from at least 540 different genes by BLASTN analyses. Approximately 25% of the subtracted clones had sequences encoding thrombospondin type-1 repeat (TSR) domains, and were derived from 17 genes. We identified 11 TSR domain-containing genes among the top 36 genes that were the most frequently detected in our SSH library. Whole-mount in situ hybridization analyses confirmed that at least 13 out of 17 TSR domain-containing genes were expressed in the hypostome of Hydra oligactis. The prominent expression of TSR domain-containing genes suggests that these genes play significant roles in the hypostome of Hydra oligactis.

RESOLUCIÓN DE CONFLICTOS AL INTERIOR DEL ORGANISMO: EL PAPEL DEL SISTEMA INMUNE

<p>El sistema inmune de los animales está constituido por una gran variedad de células y moléculas que colectivamente reconocen, neutralizan y eliminan potenciales agentes nocivos, tanto bióticos como abióticos. El estudio del sistema inmune ha estado tradicionalmente sesgado hacía algunas especies de importancia médica o económica, a expensas de la gran mayoría de especies que constituyen la diversidad animal. Con la actual facilidad de secuenciar genomas y transcriptomas, se ha abierto la posibilidad de estudiar los sistemas inmunes de muy variados grupos animales. Uno de estos grupos es los cnidarios, que incluye a los corales, anémonas y medusas, en los que el estudio del sistema inmune ha probado ser de gran utilidad para entender dos tipos de conflictos de relevancia en la supervivencia de estos organismos. El primero es la respuesta de los corales a enfermedades de carácter infeccioso y el segundo hace referencia a las reacciones de histocompatibilidad que median la competencia intraespecífica por el espacio habitable. Este artículo de reflexión trata en detalle el papel del sistema inmune de los cnidarios en la resolución de estos conflictos.</p><p> </p><p>Abstract</p><p>The immune system of animals is constituted by a large diversity of cells and molecules that collectively recognize, neutralize, and eliminate potential damaging agents, both biotic and abiotic. The study of the immune system has been traditionally biased towards some species with medical or economic importance, at the expense of the vast majority of species that constitute the animal diversity. With the current possibility of easily sequencing genomes and transcriptomes, there is an opportunity to study the immune systems of a wide variety of animal groups. One of these groups is the cnidarians, which include corals, anemones and jellyfishes, in which the study of the immune system has proved useful to understand two types of conflicts that are relevant for the survival of these organisms. The first one is the response of corals to diseases of infectious nature and the second relates to histocompatibility reactions, which mediate intraspecific competitions for habitable space. This article details the role of the cnidarian immune system to mediate the resolution of these two conflicts.</p><p> </p>

The immunotranscriptome of the Caribbean reef-building coral Pseudodiploria strigosa

The viability of coral reefs worldwide has been seriously compromised in the last few decades due in part to the emergence of coral diseases of infectious nature. Despite important efforts to understand the etiology and the contribution of environmental factors associated to coral diseases, the mechanisms of immune response in corals are just beginning to be studied systematically. In this study, we analyzed the set of conserved immune response genes of the Caribbean reef-building coral Pseudodiploria strigosa by Illumina-based transcriptome sequencing and annotation of healthy colonies challenged with whole live Gram-positive and Gram-negative bacteria. Searching the annotated transcriptome with immune-related terms yielded a total of 2782 transcripts predicted to encode conserved immune-related proteins that were classified into three modules: (a) the immune recognition module, containing a wide diversity of putative pattern recognition receptors including leucine-rich repeat-containing proteins, immunoglobulin superfamily receptors, representatives of various lectin families, and scavenger receptors; (b) the intracellular signaling module, containing components from the Toll-like receptor, transforming growth factor, MAPK, and apoptosis signaling pathways; and (3) the effector module, including the C3 and factor B complement components, a variety of proteases and protease inhibitors, and the melanization-inducing phenoloxidase. P. strigosa displays a highly variable and diverse immune recognition repertoire that has likely contributed to its resilience to coral diseases.

Adhesion networks of cnidarians: a postgenomic view

Cell-extracellular matrix (ECM) and cell-cell adhesion systems are fundamental to the multicellularity of metazoans. Members of phylum Cnidaria were classified historically by their radial symmetry as an outgroup to bilaterian animals. Experimental study of Hydra and jellyfish has fascinated zoologists for many years. Laboratory studies, based on dissection, biochemical isolations, or perturbations of the living organism, have identified the ECM layer of cnidarians (mesoglea) and its components as important determinants of stem cell properties, cell migration and differentiation, tissue morphogenesis, repair, and regeneration. Studies of the ultrastructure and functions of intercellular gap and septate junctions identified parallel roles for these structures in intercellular communication and morphogenesis. More recently, the sequenced genomes of sea anemone Nematostella vectensis, Hydra magnipapillata, and coral Acropora digitifera have opened up a new frame of reference for analyzing the cell-ECM and cell-cell adhesion molecules of cnidarians and examining their conservation with bilaterians. This chapter integrates a review of literature on the structure and functions of cell-ECM and cell-cell adhesion systems in cnidarians with current analyses of genome-encoded repertoires of adhesion molecules. The postgenomic perspective provides a fresh view on fundamental similarities between cnidarian and bilaterian animals and is impelling wider adoption of species from phylum Cnidaria as model organisms.

Involvement of L(-)-rhamnose in sea urchin gastrulation: a live embryo assay

The sea urchin embryo is a National Institutes of Health model system that has provided major developments, and is important in human health and disease. To obtain initial insights to identify glycans that mediate cellular interactions, Lytechinus pictus sea urchin embryos were incubated at 24 or 30 h post-fertilization with 0.0009-0.03 M alpha-cyclodextrin, melibiose, L(-)-rhamnose, trehalose, D(+)-xylose or L(-)-xylose in lower-calcium artificial sea water (pH 8.0, 15°C), which speeds the entry of molecules into the interior of the embryos. While α-cyclodextrin killed the embryos, and L(-)-xylose had small effects at one concentration tested, L(-)-rhamnose caused substantially increased numbers of unattached archenterons and exogastrulated embryos at low glycan concentrations after 18-24 h incubation with the sugar. The results were statistically significant compared with the control embryos in the absence of sugar (P < 0.05). The other sugars (melibiose, trehalose, D(+)-xylose) had no statistically significant effects whatsoever at any of the concentrations tested. In total, in the current study, 39,369 embryos were examined. This study is the first demonstration that uses a live embryo assay for a likely role for L(-)-rhamnose in sea urchin gastrula cellular interactions, which have interested investigators for over a century.

Neglected biological features in cnidarians self-nonself recognition

Cnidarian taxa, currently of the most morphologically simplest extant metazoans, exhibit many salient properties of innate immunity that are shared by most Animalia. One hallmark constituent of immunity exhibit by most cnidarians is histocompatibility, marked by wide spectrum of allogeneic and xenogeneic effector arms, progressing into tissue fusions or inflammatory rejections. Scientific propensity on cnidarians immunity, while discussing historecognition as the ground for immunity in these organisms, concentrates on host-parasitic and disease oriented studies, or focuses on genome approaches that search for gene homologies with the vertebrates. Above tendency for mixing up between historecognition and host-parasitic/disease, highlights a serious obstacle for the progress in our understanding of cnidarian immunobiology. Here I critically overview four 'forgotten' cnidarian immune features, namely, specificity, immunological memory, allogeneic maturation and natural chimerism, presenting insights into perspectives that are prerequisite for any discussion on cnidarian evolution. It is evident that cnidarian historecognition embraces elements that the traditional field of vertebrate immunology has never encountered (i.e., variety of cytotoxic outcomes, different types of effector mechanisms, chimerism, etc.). Also, cnidarian immune features dictating that different individuals within the same species seem to respond differently to the same immunological challenge, is far from that recorded in the vertebrates' adaptive immunity. While above features may be connected to host-parasitic and disease phenomena and effector arms, they clearly attest to their unique critical roles in shaping cnidarians historecognition, calling for improved distinction between historecognition and host-response/ disease disciplines. The research on cnidarians immunity still suffers from the lack of accepted synthesis of what historecognition is or does. Mounting of an immune response against conspecifics or xenogeneic organisms should therefore be clearly demarcated from other paths of immunity, till cnidarian innate immunity as a whole is expounded.

Diversified carbohydrate-binding lectins from marine resources

Marine bioresources produce a great variety of specific and potent bioactive molecules including natural organic compounds such as fatty acids, polysaccharides, polyether, peptides, proteins, and enzymes. Lectins are also one of the promising candidates for useful therapeutic agents because they can recognize the specific carbohydrate structures such as proteoglycans, glycoproteins, and glycolipids, resulting in the regulation of various cells via glycoconjugates and their physiological and pathological phenomenon through the host-pathogen interactions and cell-cell communications. Here, we review the multiple lectins from marine resources including fishes and sea invertebrate in terms of their structure-activity relationships and molecular evolution. Especially, we focus on the unique structural properties and molecular evolution of C-type lectins, galectin, F-type lectin, and rhamnose-binding lectin families.

Whole transcriptome profiling of successful immune response to Vibrio infections in the oyster Crassostrea gigas by digital gene expression analysis

The cultivated Pacific oyster Crassostrea gigas has suffered for decades large scale summer mortality phenomenon resulting from the interaction between the environment parameters, the oyster physiological and/or genetic status and the presence of pathogenic microorganisms including Vibrio species. To obtain a general picture of the molecular mechanisms implicated in C. gigas immune responsiveness to circumvent Vibrio infections, we have developed the first deep sequencing study of the transcriptome of hemocytes, the immunocompetent cells. Using Digital Gene Expression (DGE), we generated a transcript catalog of up-regulated genes from oysters surviving infection with virulent Vibrio strains (Vibrio splendidus LGP32 and V. aestuarianus LPi 02/41) compared to an avirulent one, V. tasmaniensis LMG 20012(T). For that an original experimental infection protocol was developed in which only animals that were able to survive infections were considered for the DGE approach. We report the identification of cellular and immune functions that characterize the oyster capability to survive pathogenic Vibrio infections. Functional annotations highlight genes related to signal transduction of immune response, cell adhesion and communication as well as cellular processes and defence mechanisms of phagocytosis, actin cytosqueleton reorganization, cell trafficking and autophagy, but also antioxidant and anti-apoptotic reactions. In addition, quantitative PCR analysis reveals the first identification of pathogen-specific signatures in oyster gene regulation, which opens the way for in depth molecular studies of oyster-pathogen interaction and pathogenesis. This work is a prerequisite for the identification of those physiological traits controlling oyster capacity to survive a Vibrio infection and, subsequently, for a better understanding of the phenomenon of summer mortality.

The evolution of the immune-type gene family Rhamnospondin in cnidarians

Rhamnose-binding lectins (RBLs) in vertebrates function in immunity as pattern recognition receptors, opsonization agents, and activators of pro-inflammatory cytokines. Although they have been identified in some invertebrate taxa, their distribution, function, and evolutionary patterns in basal metazoans, remain largely unknown. A unique RBL-containing protein composed of 8 thrombospondin type 1 repeats (TSRs) and a single RBL domain has been identified in the colonial hydroid Hydractinia symbiolongicarpus. This Rhamnospondin (Rsp) gene was specifically and constitutively expressed in the mouth of feeding polyps. Here we report the full characterization of a second Rsp gene from a H. symbiolongicarpus BAC library. Rsp1 and Rsp2 were 1.1kb apart, shared the same domain architecture and were 93% identical. Introns differed substantially in size and sequence, excepting two introns that were nearly identical, suggesting the action of inter-locus recombination. Sequencing full-length cDNAs from a wild-type individual corroborated the exon boundaries predicted from genomic DNA and showed gene polymorphism at both loci. Database searches and phylogenetic analyses showed that Rsp was found only in hydrozoans, indicating that it is an innovation of the cnidarian class Hydrozoa. Phylogenetic analysis of Rsp sequences in hydroids show a tendency of clustering paralogous genes, suggesting that they have evolved by concerted evolution.

Assembled catalog of immune-related genes from allogeneic challenged corals that unveils the participation of vWF-like transcript

While reef-building corals portray highly complex and specific allorecognition responses, still, no available synthesis on historecognition at the molecular level exists for this group of organisms. Here, we present the first subtractive library of expressed sequence tags (ESTs) from allogeneic challenged coral (Stylophora pistillata) colonies revealing the differential expression of a wide range of immune-related genes. 1760 unique ESTs were clustered and assembled into 230 contigs and 1530 singlets with 28% that showed homology (E-value < or =0.005) to known database sequences, of which 16% (n=80) homologues were identified as immune-relevant genes, encoding for stress proteins, pattern recognition receptors and complement proteins, proteases, cell adhesion proteins, cytokine related proteins, programmed cell death and proteasome-associated proteins. Transcripts that were subjected to quantitative RT-PCR, further supported the library data. In situ hybridization analyses elucidated specific and enhanced expressions of von Willebrand factor-like transcript during S. pistillata allogeneic rejection. Availability of such genome-wide expression tools may lead to significant advances in the research of coral historecognition and comparative immunology.

High amino acid diversity and positive selection at a putative coral immunity gene (tachylectin-2)

Background

Genes involved in immune functions, including pathogen recognition and the activation of innate defense pathways, are among the most genetically variable known, and the proteins that they encode are often characterized by high rates of amino acid substitutions, a hallmark of positive selection. The high levels of variation characteristic of immunity genes make them useful tools for conservation genetics. To date, highly variable immunity genes have yet to be found in corals, keystone organisms of the world's most diverse marine ecosystem, the coral reef. Here, we examine variation in and selection on a putative innate immunity gene from Oculina, a coral genus previously used as a model for studies of coral disease and bleaching.

Results

In a survey of 244 Oculina alleles, we find high nonsynonymous variation and a signature of positive selection, consistent with a putative role in immunity. Using computational protein structure prediction, we generate a structural model of the Oculina protein that closely matches the known structure of tachylectin-2 from the Japanese horseshoe crab (Tachypleus tridentatus), a protein with demonstrated function in microbial recognition and agglutination. We also demonstrate that at least three other genera of anthozoan cnidarians (Acropora, Montastrea and Nematostella) possess proteins structurally similar to tachylectin-2.

Conclusions

Taken together, the evidence of high amino acid diversity, positive selection and structural correspondence to the horseshoe crab tachylectin-2 suggests that this protein is 1) part of Oculina's innate immunity repertoire, and 2) evolving adaptively, possibly under selective pressure from coral-associated microorganisms. Tachylectin-2 may serve as a candidate locus to screen coral populations for their capacity to respond adaptively to future environmental change.

Mounting of erratic histoincompatible responses in hermatypic corals: a multi-year interval comparison

Studies on allorecognition in the phylum Cnidaria have disclosed complex arrays of effector mechanisms, specificity and competency to distinguish precisely between self and non-self attributes, and have revealed the existence of allogeneic maturity. Here we studied allo-responses between young Stylophora pistillata colonies by following 517 allogeneic interactions between naturally settled kin aggregates and by establishing 417 forced allogeneic and autogeneic assays made of solitarily settled spat that were cut into two similar size subclones, of which one had been challenged allogeneically. Fused assays were exposed to a second allorecognition challenge, made of three allogeneic types. Whereas about half of the kin allogeneic interactions led to tissue fusions and chimera formations, none of the 83 non-sibling pair combinations were histocompatible. In contrast to previous results we recorded rejections between siblings at the age of less than two months. More challenging, we documented cases of fusions between interacting siblings at ages older than one-year-old partners, all differing from a previous study made on the same coral population more than a decade ago. Similar erratic histoincompatible responses were recorded in other pocilloporid species. We suggest that these results reflect reduced genetic heterogeneity caused by chronic anthropogenic impacts on shallow water coral populations where planulae originating from the same mother colony or from different mother colonies that are genetically related share increasing parts of their genomes. Offspring born to related parents may also reveal an increase in genomic homozygosity, and altogether impose erratic alloimmunity.

The diversity of C-type lectins in the genome of a basal metazoan, Nematostella vectensis

C-type lectins (CTLs) are involved in cell-cell adhesion, recognition, and innate immunity in higher vertebrates, but little is known about CTLs in basal metazoans. The recent sequencing of the cnidarian Nematostella vectensis genome allowed us to explore the CTL-like gene family at the base of metazoan evolution. Sixty-seven predicted CTLs, with a total of 92 putative C-type lectin domains (CTLDs), were classified according to number of CTLDs present and their association with other protein domains in the CTL. Conserved residues in the glycan-binding pocket suggest that approximately half of the CTLDs retain glycan-binding function. Phylogenetic analysis of N. vectensis CTLDs with respect to other model invertebrates and humans indicates N. vectensis CTLD sequences more closely resemble vertebrate CTLDs. This study provides a N. vectensis CTL database that can be used for further research on the evolution of cnidarian CTLs and the role of CTLs in cnidarian innate immunity.

Evolution of polydom-like molecules: identification and characterization of cnidarian polydom (Cnpolydom) in the basal metazoan Hydractinia

End sequencing of random BAC clones from a Hydractinia symbiolongicarpus (Cnidaria: Hydrozoa) genomic library revealed a gene across a approximately 37.5kb region of the H. symbiolongicarpus genome sharing highest sequence identity and domain architecture to mammalian polydom that we in turn named cnidarian polydom (CnPolydom). Sharing all eight domain types characteristic of polydom and organized in a similar 5'-3' manner, CnPolydom was predicted to contain three additional domain types: PAN, FA58C, and CUB that are characteristic of CnPolydom. Expression analysis of CnPolydom from H. symbiolongicarpus (Hysy-CnPolydom) showed upregulation in response to bacterial and primarily fungal challenges, with transcripts produced specifically by a subset of interstitial stem cells (i-cells) and/or neural cells throughout the ectodermal tissue layer of feeding polyps (gastrozooids). This is the first description of a polydom-like molecule outside of Mammalia and provides evolutionary perspective on the ancestral structure and role of this pentraxin family clade.

Alternative mechanisms of immune receptor diversity

Our views of both innate and adaptive immunity have been significantly modified by recent studies of immune receptors and immunity in protostomes, invertebrate deuterostomes, and jawless vertebrates. Extraordinary variation in the means whereby organisms recognize pathogens has been revealed by a series of recent findings, including: novel forms of familiar immune receptors, high genetic polymorphism for new receptor types, germline rearrangement for non-Ig domain receptors, somatic variation of germline-encoded receptors, and unusually complex alternative splicing of genes with both immune and non-immune roles. Collectively, these observations underscore heretofore unrecognized pathways in the evolution of immune recognition and suggest universal processes by which immune systems co-opt and integrate existing cellular mechanisms to effect diverse recognition functions.