Population genetics of duplicated alternatively spliced exons of the Dscam gene in Daphnia and Drosophila

Alternatively spliced exon 33 in Dscam controls antibacterial responses through regulating cellular endocytosis and regulation of actin cytoskeleton gene expression in the hemocytes of the Chinese mitten crab (Eriocheir sinensis)

It has been widely established that Down syndrome cell adhesion molecule (Dscam) regulates arthropod cellular endocytosis. However, the signal transduction pathways and molecular mechanisms of the regulatory process remain unclear. Our previous study identified a Dscam-mediated immune signal transduction pathway that regulates cellular antimicrobial peptide expression, and a conserved endocytosis motif encoded by exon 33 in the cytoplasmic tail of transmembrane Dscam. Therefore, the present study aimed to determine the transcriptional response of the Chinese mitten crab (Eriocheir sinensis) Dscam with a cytoplasmic tail encoded by different exons. In the group of exon 32 knockdown, 306 differentially expressed genes (DEGs) were identified, and 3579 differentially expressed genes (DEGs) were identified in the group of exon 33 knockdown (green fluorescent protein, (GFP) as control). The DEGs were enriched in small molecule binding, protein-containing complex binding, and immunity-related pathways. Quantitative real-time reverse transcription PCR validated the data for selected genes. Our study contributes to the understanding of the immune defense mechanism in E. sinensis and the development of the innate immune system, thus providing insights into disease control and prevention in aquaculture.

A novel C-type lectin LvCTL 4.2 has antibacterial activity but facilitates WSSV infection in shrimp (L. vannamei)

Glycan-binding protein C-type lectin (CTL), one of the pattern recognition receptors (PRRs), binds to carbohydrates on the surface of pathogens and elicits antimicrobial responses in shrimp innate immunity. The objective was to identify and characterize a novel C-type lectin LvCTL 4.2 in Litopenaeus vannamei. The LvCTL 4.2 protein consisted of a signal peptide at the N terminal and a carbohydrate-recognition domain (CRD) with a mutated mannose-binding (Glu-Pro-Ala; EPA) motif at the C terminal, and thereby has a putative secreted mannose-binding C-type lectin architecture. LvCTL 4.2 was highly expressed in nervous tissue and stomach. Infection with white spot syndrome virus (WSSV) induced expression of LvCTL 4.2 in shrimp stomach at 12 h post infection. Conversely, there was no obvious upregulation in expression of LvCTL 4.2 in stomach or hepatopancreas of shrimp with AHPND (acute hepatopancreas necrosis disease). Pathogen binding assays confirmed recombinant LvCTL 4.2 protein (rLvCTL 4.2) had significant binding ability with the WSSV virion, Gram-negative, and Gram-positive bacteria. Moreover, rLvCTL 4.2 had strong growth inhibition of Vibrio parahaemolyticus. Silencing LvCTL 4.2 suppressed WSSV replication, whereas pretreatment of WSSV with rLvCTL 4.2 facilitated viral replication in vivo. In conclusion, LvCTL 4.2 acted as a PRR that inhibited AHPND-causing bacteria, but facilitated WSSV pathogenesis.

The gene structure and hypervariability of the complete Penaeus monodon Dscam gene

Using two advanced sequencing approaches, Illumina and PacBio, we derive the entire Dscam gene from an M2 assembly of the complete Penaeus monodon genome. The P. monodon Dscam (PmDscam) gene is ~266 kbp, with a total of 44 exons, 5 of which are subject to alternative splicing. PmDscam has a conserved architectural structure consisting of an extracellular region with hypervariable Ig domains, a transmembrane domain, and a cytoplasmic tail. We show that, contrary to a previous report, there are in fact 26, 81 and 26 alternative exons in N-terminal Ig2, N-terminal Ig3 and the entirety of Ig7, respectively. We also identified two alternatively spliced exons in the cytoplasmic tail, with transmembrane domains in exon variants 32.1 and 32.2, and stop codons in exon variants 44.1 and 44.2. This means that alternative splicing is involved in the selection of the stop codon. There are also 7 non-constitutive cytoplasmic tail exons that can either be included or skipped. Alternative splicing and the non-constitutive exons together produce more than 21 million isoform combinations from one PmDscam locus in the P. monodon gene. A public-facing database that allows BLAST searches of all 175 exons in the PmDscam gene has been established at http://pmdscam.dbbs.ncku.edu.tw/.

Pathogen-Specific Binding Soluble Down Syndrome Cell Adhesion Molecule (Dscam) Regulates Phagocytosis via Membrane-Bound Dscam in Crab

The Down syndrome cell adhesion molecule (Dscam) gene is an extraordinary example of diversity that can produce thousands of isoforms and has so far been found only in insects and crustaceans. Cumulative evidence indicates that Dscam may contribute to the mechanistic foundations of specific immune responses in insects. However, the mechanism and functions of Dscam in relation to pathogens and immunity remain largely unknown. In this study, we identified the genome organization and alternative Dscam exons from Chinese mitten crab, Eriocheir sinensis. These variants, designated EsDscam, potentially produce 30,600 isoforms due to three alternatively spliced immunoglobulin (Ig) domains and a transmembrane domain. EsDscam was significantly upregulated after bacterial challenge at both mRNA and protein levels. Moreover, bacterial specific EsDscam isoforms were found to bind specifically with the original bacteria to facilitate efficient clearance. Furthermore, bacteria-specific binding of soluble EsDscam via the complete Ig1–Ig4 domain significantly enhanced elimination of the original bacteria via phagocytosis by hemocytes; this function was abolished by partial Ig1–Ig4 domain truncation. Further studies showed that knockdown of membrane-bound EsDscam inhibited the ability of EsDscam with the same extracellular region to promote bacterial phagocytosis. Immunocytochemistry indicated colocalization of the soluble and membrane-bound forms of EsDscam at the hemocyte surface. Far-Western and coimmunoprecipitation assays demonstrated homotypic interactions between EsDscam isoforms. This study provides insights into a mechanism by which soluble Dscam regulates hemocyte phagocytosis via bacteria-specific binding and specific interactions with membrane-bound Dscam as a phagocytic receptor.

Dscam1 in Pancrustacean Immunity: Current Status and a Look to the Future

The Down syndrome cell adhesion molecule 1 (Dscam1) gene is an extraordinary example of diversity: by combining alternatively spliced exons, thousands of isoforms can be produced from just one gene. So far, such diversity in this gene has only been found in insects and crustaceans, and its essential part in neural wiring has been well-characterized for Drosophila melanogaster. Ten years ago evidence from D. melanogaster showed that the Dscam1 gene is involved in insect immune defense and work on Anopheles gambiae indicated that it is a hypervariable immune receptor. These exciting findings showed that via processes of somatic diversification insects have the possibility to produce unexpected immune molecule diversity, and it was hypothesized that Dscam1 could provide the mechanistic underpinnings of specific immune responses. Since these first publications the quest to understand the function of this gene has uncovered fascinating insights from insects and crustaceans. However, we are still far from a complete understanding of how Dscam1 functions in relation to parasites and pathogens and its full relevance for the immune system. In this Hypothesis and Theory article, we first briefly introduce Dscam1 and what we know so far about how it might function in immunity. By focusing on seven questions, we then share our sometimes contrasting thoughts on what the evidence tells us so far, what essential experiments remain to be done, and the future prospects, with the aim to provide a multiangled view on what this fascinating gene has to do with immune defense.

A depauperate immune repertoire precedes evolution of sociality in bees

Background

Sociality has many rewards, but can also be dangerous, as high population density and low genetic diversity, common in social insects, is ideal for parasite transmission. Despite this risk, honeybees and other sequenced social insects have far fewer canonical immune genes relative to solitary insects. Social protection from infection, including behavioral responses, may explain this depauperate immune repertoire. Here, based on full genome sequences, we describe the immune repertoire of two ecologically and commercially important bumblebee species that diverged approximately 18 million years ago, the North American Bombus impatiens and European Bombus terrestris.

Results

We find that the immune systems of these bumblebees, two species of honeybee, and a solitary leafcutting bee, are strikingly similar. Transcriptional assays confirm the expression of many of these genes in an immunological context and more strongly in young queens than males, affirming Bateman’s principle of greater investment in female immunity. We find evidence of positive selection in genes encoding antiviral responses, components of the Toll and JAK/STAT pathways, and serine protease inhibitors in both social and solitary bees. Finally, we detect many genes across pathways that differ in selection between bumblebees and honeybees, or between the social and solitary clades.

Conclusions

The similarity in immune complement across a gradient of sociality suggests that a reduced immune repertoire predates the evolution of sociality in bees. The differences in selection on immune genes likely reflect divergent pressures exerted by parasites across social contexts.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-015-0628-y) contains supplementary material, which is available to authorized users.

Reprint of "review of Dscam-mediated immunity in shrimp and other arthropods"

Although true adaptive immunity is only found in vertebrates, there is increasing evidence that shrimp and other arthropods exhibit immune specificity and immune memory. The invertebrate immune response is now called "innate immunity with specificity" or "immune priming", and its underlying mechanisms are still unclear. However, while vertebrate antibodies have no invertebrate homolog, the Down syndrome cell adhesion molecule (Dscam), which is a hypervariable protein created by alternative splicing, can function as a pathogen-specific recognizing molecule in arthropods. Here we review our current understanding of the Dscam-mediated immune responses in arthropods, especially in shrimp, and show that Dscam may be involved in both general innate immunity and the pathogen-specific immune response.

Dscam and pancrustacean immune memory - a review of the evidence

Evidence is accumulating for a memory-like phenomenon in the immune defence of invertebrates. Down syndrome cell adhesion molecule (Dscam) has been proposed as a key candidate for a somatically diversified receptor system in the crustaceans and insects (Pancrustacea) that could enable challenge-specific protection. However, what is the evidence for an involvement of Dscam in pancrustacean immune memory, and in particular specificity? Here we review the current state of the art, and discuss hypotheses of how Dscam could be involved in immunity. We conclude that while there is increasing evidence for the involvement of Dscam in pancrustacean immunity, crucial experiments to address whether it plays a role in specificity upon secondary encounter with a pathogen still remain to be done.

Somatic and Germline Diversification of a Putative Immunoreceptor within One Phylum: Dscam in Arthropods

Arthropod Dscam, the homologue of the human Down Syndrome cell adhesion molecule, is a receptor used by the nervous and immune systems. Unlike in vertebrates, evolutionary pressure has selected and maintained a vast Dscam diversity of isoforms, known to specifying neuronal identity during the nervous system differentiation. This chapter examines the different modes of Dscam diversification in the context of arthropods' evolution and that of their immune system, where its role is controversial. In the single Dscam gene of insects and crustaceans, mutually exclusive alternative splicing affects three clusters of duplicated exons encoding the variable parts of the receptor. The Dscam gene produces over 10,000 isoforms. In the more basal arthropods such as centipedes, Dscam diversity results from a combination of many germline genes (over 80) with, in about half of those, the possibility of alternative splicing affecting only one exon cluster. In the even more basal arthropods, such as chelicerates, no splicing possibility is detected, but there exist dozens of germline Dscam genes. Compared to controlling the expression of multiple germline genes, the somatic mutually alternative splicing within a single gene may offer a simplified way of expressing a large Dscam repertoire. Expressed by hemocytes, Dscam is considered a phagocytic receptor but is also encountered in solution. More information is necessary about its binding to pathogens, its role in phagocytosis, its possible role in specifying hemocyte identity, its kinetics of expression, and the regulation of its RNA splicing to understand how its diversity is linked to immunity.

Review of Dscam-mediated immunity in shrimp and other arthropods

Although true adaptive immunity is only found in vertebrates, there is increasing evidence that shrimp and other arthropods exhibit immune specificity and immune memory. The invertebrate immune response is now called "innate immunity with specificity" or "immune priming", and its underlying mechanisms are still unclear. However, while vertebrate antibodies have no invertebrate homolog, the Down syndrome cell adhesion molecule (Dscam), which is a hypervariable protein created by alternative splicing, can function as a pathogen-specific recognizing molecule in arthropods. Here we review our current understanding of the Dscam-mediated immune responses in arthropods, especially in shrimp, and show that Dscam may be involved in both general innate immunity and the pathogen-specific immune response.

Variable immune molecules in invertebrates

Recently it has become evident that invertebrates may mount a highly variable immune response that is dependent on which pathogen is involved. The molecular mechanisms behind this diversity are beginning to be unravelled and in several invertebrate taxa immune proteins exhibiting a broad range of diversity have been found. In some cases, evidence has been gathered suggesting that this molecular diversity translates into the ability of an affected invertebrate to mount a defence that is specifically aimed at a particular pathogen.

Properties of Litopenaeus vannamei Dscam (LvDscam) isoforms related to specific pathogen recognition

Arthropod Down syndrome cell adhesion molecules (Dscam) may sometimes function as hypervariable pathogen recognition receptors. They consist of an extracellular region and a cytoplasmic tail, both of which are highly variable. In shrimp, tail-less Dscam proteins (Dscams) have recently been identified, and these appear to be unlike other arthropod extracellular Dscams that are released from the cell membrane by proteolytic cleavage. Here we investigate the properties of these unique shrimp proteins and show that they can be directly secreted from transfected cells. We also investigate the diverse cytoplasmic tail variants of membrane-bound shrimp Dscams, and show that elements E1A and E3 seem to be related to Dscam immune function. Challenge with Vibrio harveyi not only enhanced total Dscam and the immune-related cytoplasmic tail variants, but also induced expression of certain Ig2 + Ig3 combinations. A pathogen binding assay with these Ig2 + Ig3 extracellular variants showed that both the V. harveyi-induced Dscams and Dscams induced by buffer injection could be either pathogen-specific or specific only for Gram-negative pathogens, while other "general" Dscam variants were sensitive to a wide range of pathogens. The same assay also suggested that shrimp Dscam isoforms show a stronger response to the host's natural pathogens.

A tailless Dscam from Eriocheir sinensis diversified by alternative splicing

Dscam (Down syndrome cell adhesion molecule), a member of the immunoglobulin superfamily (IgSF), plays an essential role in pathogen recognition and further involves in the innate defense of invertebrates. In the present study, the cDNA of a Dscam from Chinese mitten crab Eriocheir sinensis (designated EsDscam) was cloned and characterized. It contained a 5-terminal untranslated region (UTR) of 60 bp, a 3-UTR of 216 bp with a poly (A) tail, and an open reading frame (ORF) of 4848 bp encoding a polypeptide of 1615 amino acids with the putative molecular mass of 178.4 kDa and theoretical isoelectric point of 6.31. The EsDscam protein shared higher sequence identities and similar domain architecture with Dscams from other invertebrate, including typical 10 immunoglobulin (Ig) domains, 6 fibronectin type 3 domains (FNIII) and one cell attachment sequence (RGD) in extracellular region, while it lacked the expected transmembrane domain and cytoplasmic tail compared with other members of Dscam family. After sequencing 80 separate clones of Ig2, 3 and Ig7 regions from pooled cDNA libraries constructed from normal and bacterial-infected crabs, 44 alternative sequences were detected in the N-terminal of Ig2, 39 ones in Ig3, and 31 ones in Ig7 domain, suggesting that EsDscam could potentially encode at least 53196 unique isoforms. Furthermore, two 3'UTR isoforms and two 5'UTR isoforms of EsDscam were also identified by RACE strategy. EsDscam mRNA was most abundantly expressed in the tissues of nerve, muscle, hepatopancreas and gill, and weakly expressed in heart, gonad and hemocytes. Western blotting and immunofluorescence analysis revealed that EsDscam protein was mainly distributed in serum, and few on the membrane of crab hemocytes. These results suggested that this tailless EsDscam was one member of crustacean Dscam family, and the generation of diverse isoforms through alternative splicing allowed it to recognize various pathogens and play an active role in immune defense of crabs.

More than one way to produce protein diversity: duplication and limited alternative splicing of an adhesion molecule gene in basal arthropods

Exon duplication and alternative splicing evolved multiple times in metazoa and are of overall importance in shaping genomes and allowing organisms to produce many fold more proteins than there are genes in the genome. No other example is as striking as the one of the Down syndrome cell adhesion molecule (Dscam) of insects and crustaceans (pancrustaceans) involved in the nervous system differentiation and in the immune system. To elucidate the evolutionary history of this extraordinary gene, we investigated Dscam homologs in two basal arthropods, the myriapod Strigamia maritima and the chelicerate Ixodes scapularis. In both, Dscam diversified extensively by whole gene duplications resulting in multigene expansions. Within some of the S. maritima genes, exons coding for one of the immunoglobulin domains (Ig7) duplicated and are mutually exclusively alternatively spliced. Our results suggest that Dscam diversification was selected independently in chelicerates, myriapods, and pancrustaceans and that the usage of Dscam diversity by immune cells evolved for the first time in basal arthropods. We propose an evolutionary scenario for the appearance of the highly variable Dscam gene of pancrustaceans, adding to the understanding of how alternative splicing, exon, and gene duplication contribute to create molecular diversity associated with potentially new cellular functions.

The evolution of Dscam genes across the arthropods

BACKGROUND

One way of creating phenotypic diversity is through alternative splicing of precursor mRNAs. A gene that has evolved a hypervariable form is Down syndrome cell adhesion molecule (Dscam-hv), which in Drosophila melanogaster can produce thousands of isoforms via mutually exclusive alternative splicing. The extracellular region of this protein is encoded by three variable exon clusters, each containing multiple exon variants. The protein is vital for neuronal wiring where the extreme variability at the somatic level is required for axonal guidance, and it plays a role in immunity where the variability has been hypothesised to relate to recognition of different antigens. Dscam-hv has been found across the Pancrustacea. Additionally, three paralogous non-hypervariable Dscam-like genes have also been described for D. melanogaster. Here we took a bioinformatics approach, building profile Hidden Markov Models to search across species for putative orthologs to the Dscam genes and for hypervariable alternatively spliced exons, and inferring the phylogenetic relationships among them. Our aims were to examine whether Dscam orthologs exist outside the Bilateria, whether the origin of Dscam-hv could lie outside the Pancrustacea, when the Dscam-like orthologs arose, how many alternatively spliced exons of each exon cluster were present in the most common recent ancestor, and how these clusters evolved.

RESULTS

Our results suggest that the origin of Dscam genes may lie after the split between the Cnidaria and the Bilateria and supports the hypothesis that Dscam-hv originated in the common ancestor of the Pancrustacea. Our phylogeny of Dscam gene family members shows six well-supported clades: five containing Dscam-like genes and one containing all the Dscam-hv genes, a seventh clade contains arachnid putative Dscam genes. Furthermore, the exon clusters appear to have experienced different evolutionary histories.

CONCLUSIONS

Dscam genes have undergone independent duplication events in the insects and in an arachnid genome, which adds to the more well-known tandem duplications that have taken place within Dscam-hv genes. Therefore, two forms of gene expansion seem to be active within this gene family. The evolutionary history of this dynamic gene family will be further unfolded as genomes of species from more disparate groups become available.