Structural and functional characterization of complement C4 and C1s-like molecules in teleost fish: insights into the evolution of classical and alternative pathways

An Introduction to Relevant Immunology Principles with Respect to Oral Vaccines in Aquaculture

Vaccines continue to play an enormous role in the progression of aquaculture industries worldwide. Though preventable diseases cause massive economic losses, injection-based vaccine delivery is cost-prohibitive or otherwise impractical for many producers. Most oral vaccines, which are much cheaper to administer, do not provide adequate protection relative to traditional injection or even immersion formulas. Research has focused on determining why there appears to be a lack of protection afforded by oral vaccines. Here, we review the basic immunological principles associated with oral vaccination before discussing the recent progress and current status of oral vaccine research. This knowledge is critical for the development and advancement of efficacious oral vaccines for the aquaculture industry.

Identification of key overlapping DEGs and molecular pathways under multiple stressors in the liver of Nile tilapia (Oreochromis niloticus)

The identification of key genes and molecular pathways that are involved in the response to stressors is crucial for controlling stress in fish and sustainable aquaculture. Environmental stressors can induce stress responses in aquatic animals, resulting in compromised immune function, inhibited growth, and increased mortality rates. mRNA-seq analysis provides a powerful tool to identify key genes and pathways associated with stress response. In the present study, mRNA-seq analysis was employed to identify key overlapping differentially expressed genes (DEGs) and molecular pathways under salinity, nitrite, copper, and pH stress in the liver of Nile tilapia (Oreochromis niloticus). The pathways associated with the immune response, oxygen transport, homeostasis, and oxidative stress were enriched across all stressors. The top KEGG pathways were complement and coagulation cascades, PPAR signaling pathway, and cardiac muscle contraction. The top GO enrichment terms were oxidoreductase activity, aerobic respiration, endopeptidase inhibitor activity, endopeptidase regulator activity, heme binding, and iron ion binding. The complement genes (C3, C4, C5, factor B, and factor H), alpha-2-macroglobulin (A2M), hemoglobin subunit epsilon (HBE), hemoglobin subunit alpha (HBA), coagulation factor genes (XI and X) and the cytochrome c oxidase (COX) gene family (cox1, cox2, cox3, cytochrome P450) were identified as key shared genes across multiple stressors. The discovery of these genes and molecular pathways provided a better understanding of the molecular mechanism underlying the stress response in Nile tilapia. The results of the present study can facilitate the development of stress management strategies in Nile tilapia.

Modulatory effect of thymol on the immune response and susceptibility to Aeromonas hydrophila infection in Nile tilapia fish exposed to zinc oxide nanoparticles

Zinc oxide nanoparticles (ZnO-NPs) have many exciting properties that make their use in a continuous increase in various biomedical, industrial, and agricultural applications. This is associated with accumulation in the aquatic ecosystems and fish exposure with consequent deleterious effects. To determine the potential of thymol to counteract the immunotoxic effects of ZnO-NPs, Oreochromis niloticus was exposed to ZnO-NPs (⅕ LC₅₀ =1.14 mg/L, for 28 days) with or without feeding a thymol-incorporated diet (1 or 2 g/kg diet). Our data demonstrated a reduction of aquaria water quality, leukopenia, and lymphopenia with a decrease in serum total protein, albumin, and globulin levels in exposed fish. At the same time, the stress indices (cortisol and glucose) were elevated in response to ZnO-NPs exposure. The exposed fish also revealed a decline in serum immunoglobulins, nitric oxide, and the activities of lysozyme and myeloperoxidase, in addition to reduced resistance to the Aeromonas hydrophila challenge. The RT-PCR analysis showed downregulation of antioxidant (SOD) superoxide dismutase and (CAT) catalase gene expression in the liver tissue with overexpression of the immune-related genes (TNF-α and IL-1β). Importantly, we found that thymol markedly protected against ZnO-NPs-induced immunotoxicity in fish co-supplemented with thymol (1 or 2 g/kg diet) in a dose-dependent manner. Our data confirm the immunoprotective and antibacterial effects of thymol in ZnO-NPs exposed fish, supporting the potential utility of thymol as a possible immunostimulant agent.

Efficacy and transcriptome analysis of golden pompano (Trachinotus ovatus) immunized with a formalin-inactived vaccine against Streptococcus iniae

Streptococcus iniae is a worldwide fish pathogen that cause tremendous economic losses to the global aquaculture industry. Vaccination is regarded as the most effective and safe way to control fish diseases. In our study, we developed a formalin-inactivated vaccine against S. iniae and evaluated its effect in golden pompano (Trachinotus ovatus). In addition, in order to clarify the molecular mechanisms underlying the vaccine protection, we compared the spleen transcriptomes of vaccinated and unvaccinated golden pompano at 1, 2 and 7 d post vaccination using the RNA-seq technology. The relative percentage survival (RPS) reached 71.1% at 28 days post-vaccination which suggested that the vaccine provided highly protection against S. iniae. KEGG pathway analysis revealed that phagosome, cytokine-cytokine receptor interaction, MAPK signaling pathway, and CAMs were activated by the vaccine. The most of strongly up-regulated genes in golden pompano spleen are involving in innate immunity. For adaptive immunity, the vaccine evoked a CD8⁺ CTL-mediated response by MHC Ⅰ pathway to achieve immune protection.

An overview of complement systems in teleosts

Complement plays an important role in the innate immune system, and it comprises about 35 individual proteins. In mammals, complement is activated via three different pathways, the classical pathway, the alternative pathway, and the lectin pathway. All three activation pathways produce C3-convertase in different forms. C3-convertase cleaves C3 to C3a and C3b and initiates a cascade of cleavage and activation, eventually resulting in the formation of the membrane attack complex. Complement activation results in the generation of activated fragments that are involved in microbial killing, phagocytosis, inflammatory reactions, immune complex clearance, and antibody production. Although the complement system has been studied extensively in mammals, complement is less well understood in teleosts. This review summarizes the current knowledge of the teleost complement components involved in phagocytosis, chemotaxis, and cell lysis. We report the characterized complement components in various teleost species. In addition, we provide a comprehensive compilation of complement regulators, and this information is used to analyze the role of complement regulators in pathogen infection. The influence of complement receptors on the immune responses of teleosts is reviewed. Finally, we propose directions for future study of the molecular evolution, structure, and function of complement components in teleosts. This review provides new insights into the complement system of recognition and defense, and such knowledge is essential for the development of new immune strategies in aquaculture.

Immune response of silver pomfret (Pampus argenteus) to Amyloodinium ocellatum infection

Amyloodinium ocellatum (AO) infection in silver pomfret (Pampus argenteus) causes extensive mortality. Insufficient information exists on the molecular immune response of silver pomfret to AO infestation, so herein we simulated the process of silver pomfret being infected by AO. Translucent trophosomes were observed on the gills of AO-infected fish. Transcriptome profiling was performed to investigate the effects of AO infection on the gill, kidney complex and spleen. Overall, 404,412,298 clean reads were obtained, assembling into 96,341 unigenes, which were annotated against public databases. In total, 2730 differentially expressed genes were detected, and few energy- and immune-related genes were further assessed using RT-qPCR. Moreover, activities of three immune-related (SOD, AKP and ACP) and three energy-related (PKM, LDH and GCK) enzymes were determined. AO infection activated the immune system and increased interleukin-1 beta and immunoglobulin M heavy chain levels. Besides, the PPAR signalling pathway was highly enriched, which played a role in improving immunity and maintaining homeostasis. AO infection also caused dyspnoea, leading to extensive lactic acid accumulation, potentially contributing towards a strong immune response in the host. Our data improved our understanding regarding the immune response mechanisms through which fish coped with parasitic infections and may help prevent high fish mortality in aquaculture.

Transcriptome and co-expression network analyses reveal the regulatory pathways and key genes associated with temperature adaptability in the yellow drum (Nibea albiflora)

The yellow drum (Nibea albiflora) is an important marine economy fish, that is widely distributed in the coastal waters of the Northwest Pacific. To understand the molecular regulatory mechanism of the yellow drum under temperature stress, transcriptome analysis was performed under five temperature conditions (10 °C, 15 °C, 20 °C, 24 °C, 28 °C) in the present study. Compared with 20 °C, 163, 401, 276, and 372 differentially expressed genes (DEGs) were obtained at 10 °C, 15 °C, 24 °C and 28 °C, respectively. Gene Ontology (GO) analysis indicated that the DEGs were mainly involved in cellular processes, metabolic processes, catalytic activity, membrane and binding. Meanwhile, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the temperature adaptive regulation of the yellow drum was mainly involved in signal transduction, metabolism, genetic information and protein processing. Weighted gene co-expression network analysis (WGCNA) showed that HMGB1, STAT4, Noct, C1q and CRT may be the key hub genes in the response of the yellow drum to temperature stress. In addition, 20 genes that may be associated with temperature stress were identified based on comparative analysis between the KEGG enrichment and the WGCNA results. Ten DEGs were selected for further validation using quantitative real-time PCR (qRT-PCR), and the results were consistent with the RNA-seq data. This study explored the transcriptional patterns of the yellow drum under temperature stress and provided fundamental information on the temperature adaptability of this species.

Mucosal immunoglobulins of teleost fish: A decade of advances

Immunoglobulins (Igs) are complex glycoproteins that play critical functions in innate and adaptive immunity of all jawed vertebrates. Given the unique characteristics of mucosal barriers, secretory Igs (sIgs) have specialized to maintain homeostasis and keep pathogens at bay at mucosal tissues from fish to mammals. In teleost fish, the three main IgH isotypes, IgM, IgD and IgT/Z can be found in different proportions at the mucosal secretions of the skin, gills, gut, nasal, buccal, and pharyngeal mucosae. Similar to the role of mammalian IgA, IgT plays a predominant role in fish mucosal immunity. Recent studies in IgT have illuminated the primordial role of sIgs in both microbiota homeostasis and pathogen control at mucosal sites. Ten years ago, IgT was discovered to be an immunoglobulin class specialized in mucosal immunity. Aiming at this 10-year anniversary, the goal of this review is to summarize the current status of the field of fish Igs since that discovery, while identifying knowledge gaps and future avenues that will move the field forward in both basic and applied science areas.

Adaptive immune responses in channel catfish exposed to Edwardsiella ictaluri live attenuated vaccine and wild type strains through the specific gene expression profiles

We extend the previous findings on the differential activity of immune-related genes in the lymphoid organs of channel catfish in the 7 days post-challenge (dpc) with E. ictaluri live attenuated vaccines (LAVs) and wild type (WT) strains by assessing the expression of these genes in the 21 dpc. The expression of T and B cell-specific genes were significantly elevated in the spleen at 14 dpc and in the AK at 21 dpc in catfish treated with E. ictaluri WT and LAV strains compared to a non-treated control group. The gene expression of IFN-γ correlated with adaptive immunity genes in the lymphoid tissues of catfish. These data indicate that two novel LAVs were able to trigger the activation of T helper1 polarization cytokine IFN-γ gene and specific lymphocyte genes in the spleen followed by their activation in the AK of catfish without causing inflammation, thus providing protective immunity in E. ictaluri infection.

Immunoglobulins in teleosts

Immunoglobulins are glycoproteins which are produced as membrane-bound receptors on B-cells or in a secreted form, known as antibodies. In teleosts, three immunoglobulin isotypes, IgM, IgT, and IgD, are present, each comprising two identical heavy and two identical light polypeptide chains. The basic mechanisms for generation of immunoglobulin diversity are similar in teleosts and higher vertebrates. The B-cell pre-immune repertoire is diversified by VDJ recombination, junctional flexibility, addition of nucleotides, and combinatorial association of light and heavy chains, while the post-immune repertoire undergoes somatic hypermutation during clonal expansion. Typically, the teleost immunoglobulin heavy chain gene complex has a modified translocon arrangement where the Dτ-Jτ-Cτ cluster of IgT is generally located between the variable heavy chain (VH) region and the Dμ/δ-Jμ/δ-Cμ-Cδ gene segments, or within the set of VH gene segments. However, multiple genome duplication and deletion events and loss of some individual genes through evolution has complicated the IgH gene organization. The IgH gene arrangement allows the expression of either IgT or IgM/IgD. Alternative splicing is responsible for the regulation of IgM/IgD expression and the secreted versus transmembrane forms of IgT, IgD, and IgM. The overall structure of IgM and IgT is usually conserved across species, whereas IgD has a large variety of structures. IgM is the main effector molecule in both systemic and mucosal immunity and shows a broad range of concentrations in different teleost species. Although IgM is usually present in higher concentrations under normal conditions, IgT is considered the main mucosal Ig.

Toxicological responses of Carassius auratus induced by benzophenone-3 exposure and the association with alteration of gut microbiota

Gut microbiota plays a fundamental role in host's physiology. However, the effect of organic UV filters, an emerging contaminant on gut microbiota is poorly understood. Here, fish (Carassius auratus) were exposed to 2, 20 and 200 μg/L of benzophenone-3 (BP3) for 28 days to explore the toxicological effects and its association with the changes in the gut microbiota. The BP3 accumulation is time and dose dependent in the liver and intestine. Under BP3 subchronic exposure, fish's body and intestinal weights, reactive oxygen species (ROS), immunoglobulin M (IgM) and vitellogenin (VTG) levels, as well as 7-benzyloxy-4-trifluoromethylcoumarin-O-debenzyloxylase (BFCOD) activities, were decreased. BP3 exposure has increased the abundance of Bacteroidetes phylum and Mycobacterium genus. Bioinformatic analysis revealed that the levels of ROS, IgM, estrogen receptor and VTG, activities of lysozyme, BFCOD and 7-ethoxyresorufin-O-deethylase were significantly correlated with the relative abundance of intestinal microbial genus (p < 0.05). These results highlight for the first time the association between the effects of organic UV filters on the antioxidant, immune, endocrine, and metabolic systems of the fish and changes in the gut microbiota, which extend knowledge of the role of gut microbiota in ecotoxicology.

Identification, characterization, and immunological analysis of complement component 4 from grass carp (Ctenopharyngodon idella)

Complement component 4 (C4) has critical immunological functions in vertebrates. In the current study, a C4 homolog (gcC4) was identified in grass carp (Ctenopharyngodon idella). The full-length 5458 bp gcC4 cDNA contained a 5148 bp open reading frame (ORF) encoding a protein of 1715 amino acids with a signal peptide and eight conservative domains. The gcC4 protein has a high level of identity with other fish C4 counterparts and is phylogenetically clustered with cyprinid fish C4. The gcC4 transcript shows wide tissue distribution and is inducible by Aeromonas hydrophila in vivo and in vitro. Furthermore, its expression also fluctuates upon lipopolysaccharide or flagellin stimulation in vitro. During infection, the gcC4 protein level decreases or increases to varying degrees, and the intrahepatic C4 expression location changes. With gcC4 overexpression, interleukin 1 beta, tumor necrosis factor alpha, and interferon transcripts are all upregulated by A. hydrophila infection. Meanwhile, overexpression of gcC4 reduces bacterial invasion or proliferation. Moreover, gcC4 may activate the NF-κB signaling pathway. These findings demonstrate the vital role of gcC4 in the innate immunity of grass carp.

Complement proteins detected through iTRAQ-based proteomics analysis of serum from black carp Mylopharyngodon piceus in response to experimentally induced Aeromonas hydrophila infection

The black carp Mylopharyngodon piceus is one of the culturally important '4 famous domestic fishes' in China. Recently, infectious diseases caused by Aeromonas hydrophila have drastically altered the operation of the black carp farming industry. In the present study, isobaric tags for relative and absolute quantitation (iTRAQ) were combined with mass spectrometry analysis to screen for differentially abundant black carp serum proteins in response to experimentally induced A. hydrophila infection. A total of 86 differentially abundant proteins were quantified at 24 h post-infection, including 78 down-regulated proteins and 8 up-regulated proteins. The down-regulated proteins included complement C1q subcomponent subunit C, complement factor B/C2A, complement factor B/C2B, complement C3-Q1, complement C3, and complement C4-2. Bioinformatic analysis indicated that the differentially abundant proteins were mainly associated with complement and coagulation cascades (27.9%). Moreover, real-time PCR (qPCR) analysis revealed changes in the gene expression of both C3 and B/C2A in blood cells, liver, kidney, gills, and intestines of the black carp infected with A. hydrophila. However, mRNA expression levels did not consistently correlate with the corresponding protein levels. A polyclonal antibody was prepared using a synthetic C3 peptide. Immunofluorescence analysis showed that the expression of C3 in the kidney was increased with A. hydrophila infection. This work provides a useful characterization of the impact of A. hydrophila infection on the complement system of the black carp.

Effect of Light–Dark Cycle on Skin Mucosal Immune Activities of Gilthead Seabream (Sparus aurata) and European Sea Bass (Dicentrarchus labrax)

Changes in different immune activities in the skin mucus of gilthead seabream (Sparus aurata L.) and European sea bass (Dicentrarchus labrax L.) specimens exposed to a constant light–dark photoperiod (12 h L:12 h D) were studied. Samples were collected at 08:00 (light on), 14:00, 20:00 (light off), 02:00, and again at 08:00 to determine immunoglobulin M (IgM) levels, several enzymes related to the immune system, and bactericidal activity. IgM levels were higher during the day in seabream and reached a minimum value at 20:00, but it was hardly affected in sea bass. No significant variations were recorded in the levels of protease and antiprotease. Peroxidase reached its maximum level in seabream at 02:00, the same time that it reached its minimum level in sea bass. Lysozyme showed little variation in seabream, but it was significantly lower at 14:00 than during the rest of the cycle in sea bass. Finally, different interspecific variations on bactericidal activity against Vibrio harveyi were recorded. The findings demonstrate that the immune parameters present in skin mucus of these important fish species are affected by the light–dark cycle and that there are substantial interspecies differences.

Complement component C4-like protein in Atlantic cod (Gadus morhua L.) - Detection in ontogeny and identification of post-translational deimination in serum and extracellular vesicles

The complement system is a critical part of teleost immune defences, with complement component C4 forming part of the classical and lectin pathways. Cod C4-like protein was isolated from plasma, specific antibodies generated and C4-like protein was assessed in cod sera, mucus and in extracellular vesicles (EVs) from serum and mucus. Higher levels of C4-like protein were detected in serum- than mucus-derived EVs. Post-translational deimination, caused by conversion of arginine into citrulline, can affect protein structure and function. Here we detected deiminated forms of C4-like protein in cod serum and at lower levels in mucus. C4-like protein was also found in deiminated form at low levels in EVs from both serum and mucus. C4-like protein was assessed by immunohistochemistry in cod larvae and detected in a range of organs including in liver, kidney, gut, muscle, skin and mucus, as well as in neuronal tissues of the brain, spinal cord and eye. This abundance of C4-like protein during early development may indicate roles in tissue remodelling, in addition to immune defences. The presence of deiminated C4-like protein in serum and mucosa, as well as in EVs, may suggest C4 protein moonlighting via post-translational deimination.

Mass spectrometric determination of disulfide bonds and free cysteine in grass carp IgM isoforms

Disulfide bonds are fundamental in establishing Ig structure and maintaining Ig biological function. Here, we analysed disulfide bonds and free cysteine in three grass carp IgM isoforms (monomeric, dimeric/trimeric, and tetrameric IgM) by liquid chromatography-electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS). The results revealed that Cys⁵⁷⁴ residue status at the C-terminal tail differed substantially in monomeric IgM in comparison with polymeric IgM, Cys⁵⁷⁴ was found as free thiol in monomeric IgM, while it formed disulfide linkages in dimeric/trimeric and tetrameric IgM. Five intra-chain disulfide bonds in the CH1~CH4 and CL1 domains, as well as one H-H and one H-L inter-chain disulfide linkages, were also observed and shown identical connectivity in monomeric, dimeric/trimeric, and tetrameric IgM. These findings represent the first experimental assignments of disulfide linkages of grass carp IgM and reveal that grass carp IgM isoform formation is due to alternative disulfide bonds connecting the Cys⁵⁷⁴ residue at the C-terminal tail.

Protective effects of seaweed supplemented diet on antioxidant and immune responses in European seabass (Dicentrarchus labrax) subjected to bacterial infection

European seabass (Dicentrarchus labrax) production is often hampered by bacterial infections such as photobacteriosis caused by Photobacterium damselae subsp. piscicida (Phdp). Since diet can impact fish immunity, this work investigated the effect of dietary supplementation of 5% Gracilaria sp. aqueous extract (GRA) on seabass antioxidant capacity and resistance against Phdp. After infection, mortality was delayed in fish fed GRA, which also revealed increased lysozyme activity levels, as well as decreased lipid peroxidation, suggesting higher antioxidant capacity than in fish fed a control diet. Dietary GRA induced a down-regulation of hepatic stress-responsive heat shock proteins (grp-78, grp-170, grp-94, grp-75), while bacterial infection caused a down-regulation in antioxidant genes (prdx4 and mn-sod). Diet and infection interaction down-regulated the transcription levels of genes associated with oxidative stress response (prdx5 and gpx4) in liver. In head-kidney, GRA led to an up-regulation of genes associated with inflammation (il34, ccr9, cd33) and a down-regulation of genes related to cytokine signalling (mif, il1b, defb, a2m, myd88). Additionally, bacterial infection up-regulated immunoglobulins production (IgMs) and down-regulated the transcription of the antimicrobial peptide leap2 in head kidney. Overall, we found that GRA supplementation modulated seabass resistance to Phdp infection.

Aeromonas hydrophila suppresses complement pathways via degradation of complement C3 in bony fish by metalloprotease

Aeromonas hydrophila is a pathogen that causes high mortality in the grass carp. The complement system, as a frontline defence of innate immunity, plays an important role in the immune response against pathogens. However, the immunity evasion mechanism of A. hydrophila against the complement system of grass carp remains unclear. In this study, we described an additional mechanism used by A. hydrophila GD18 to evade the complement system and survive in grass carp serum. First, A. hydrophila evaded the bactericidal activity of grass carp serum. Second, the haemolytic activity assays showed that A. hydrophila obviously suppressed the alternative pathway, which depended on preventing the formation or disabling the function of the membrane-attack complex (MAC). Further research indicated that A. hydrophila targeted complement C3, the central component of the three complement pathways, and degraded it in the grass carp serum, leading to the inhibition of the complement pathways, which resulted in the serum-resistance of A. hydrophila. Furthermore, cleavage analyses showed that extracellular proteases (ECPases) of A. hydrophila efficiently cleaved purified C3 as well as C3 in grass carp serum. Finally, protease inhibitor studies and mass spectrum analysis identified the secreted metalloprotease elastase (AhE), which was present in large amounts in crude ECPases, as the central molecule responsible for C3 cleavage. Compared to wild strain GD18, the AhE knockout, Δahe was dramatically reduced in the ability of serum resistance. Our findings suggested that A. hydrophila escaped serum-killing by suppressing the complement pathways via the degradation of complement C3 in bony fish, which was related to secreted metalloproteases.

A Comparison of the Innate and Adaptive Immune Systems in Cartilaginous Fish, Ray-Finned Fish, and Lobe-Finned Fish

The immune system is composed of two subsystems-the innate immune system and the adaptive immune system. The innate immune system is the first to respond to pathogens and does not retain memory of previous responses. Innate immune responses are evolutionarily older than adaptive responses and elements of innate immunity can be found in all multicellular organisms. If a pathogen persists, the adaptive immune system will engage the pathogen with specificity and memory. Several components of the adaptive system including immunoglobulins (Igs), T cell receptors (TCR), and major histocompatibility complex (MHC), are assumed to have arisen in the first jawed vertebrates-the Gnathostomata. This review will discuss and compare components of both the innate and adaptive immune systems in Gnathostomes, particularly in Chondrichthyes (cartilaginous fish) and in Osteichthyes [bony fish: the Actinopterygii (ray-finned fish) and the Sarcopterygii (lobe-finned fish)]. While many elements of both the innate and adaptive immune systems are conserved within these species and with higher level vertebrates, some elements have marked differences. Components of the innate immune system covered here include physical barriers, such as the skin and gastrointestinal tract, cellular components, such as pattern recognition receptors and immune cells including macrophages and neutrophils, and humoral components, such as the complement system. Components of the adaptive system covered include the fundamental cells and molecules of adaptive immunity: B lymphocytes (B cells), T lymphocytes (T cells), immunoglobulins (Igs), and major histocompatibility complex (MHC). Comparative studies in fish such as those discussed here are essential for developing a comprehensive understanding of the evolution of the immune system.

Do the toll-like receptors and complement systems play equally important roles in freshwater adapted Dolly Varden char (Salvelinus malma)?

Unlike the normal anadromous lifestyle, Chinese native Dolly Varden char (Salvelinus malma) is locked in land and lives in fresh water lifetime. To explore the effect of freshwater adaption on its immune system, we constructed a pooled cDNA library of hepatopancreas and spleen of Chinese freshwater Dolly Varden char (S. malma). A total of 27,829 unigenes were generated from 31,233 high-quality transcripts and 17,670 complete open reading frames (ORF) were identified. Totally 25,809 unigenes were successfully annotated and it classified more native than adaptive immunity-associated genes, and more genes involved in toll-like receptor signal pathway than those in complement and coagulation cascades (51 vs 3), implying the relative more important role of toll-like receptors than the complement system under bacterial injection for the freshwater Dolly Varden char. These huge different numbers of TLR and complement system identified in freshwater Dolly Varden char probably caused by distinct evolution pressure patterns between fish TLR and complement system, representative by TLR3 and TLR5 as well as C4 and C6, respectively, which were under purifying and positively selecting pressure, respectively. Further seawater adaptation experiment and the comparison study with our library will no doubt be helpful to elucidate the effect of freshwater adaption of Chinese native Dolly Varden char on its immune system.

Label-free quantification of protein expression in the rainbow trout (Oncorhynchus mykiss) in response to short-term exposure to heat stress

Rainbow trout (Oncorhynchus mykiss) are a cold-water salmonid species that is highly susceptible to heat stress. Summer temperature stress is a common issue in trout aquaculture. To better understand the molecular mechanisms of the heat-stress response in the trout, we used label-free quantitative proteome techniques to identify differentially expressed proteins in the livers of rainbow trout exposed to heat stress. We identified 3362 proteins and 152 differentially expressed proteins (p < 0.05; fold-change >2). Of these, 37 were uniquely expressed in the heat-stress group and 35 were uniquely expressed in the control group. In addition, 42 proteins were significantly upregulated (fold-change >2) and 38 proteins were significantly downregulated (fold-change >2). GO (Gene Ontology) analysis indicated that these differentially expressed proteins were primarily expressed in the nucleus, extracellular matrix, and cytoplasm, and were associated with a variety of functions, including protein binding/bridging and enzyme facilitation. KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis of the differentially expressed proteins showed that, during high temperature stress, many biological processes were extensively altered, particularly the estrogen signaling pathway, the complement and coagulation cascades, and the platelet activation pathway. Our study focused on the identification of a systematic approach for the characterization of regulatory networks. Our results provide a framework for further studies of the heat-stress response in fish.

Peptidylarginine deiminase and deiminated proteins are detected throughout early halibut ontogeny - Complement components C3 and C4 are post-translationally deiminated in halibut (Hippoglossus hippoglossus L.)

Post-translational protein deimination is mediated by peptidylarginine deiminases (PADs), which are calcium dependent enzymes conserved throughout phylogeny with physiological and pathophysiological roles. Protein deimination occurs via the conversion of protein arginine into citrulline, leading to structural and functional changes in target proteins. In a continuous series of early halibut development from 37 to 1050° d, PAD, total deiminated proteins and deiminated histone H3 showed variation in temporal and spatial detection in various organs including yolksac, muscle, skin, liver, brain, eye, spinal cord, chondrocytes, heart, intestines, kidney and pancreas throughout early ontogeny. For the first time in any species, deimination of complement components C3 and C4 is shown in halibut serum, indicating a novel mechanism of complement regulation in immune responses and homeostasis. Proteomic analysis of deiminated target proteins in halibut serum further identified complement components C5, C7, C8 C9 and C1 inhibitor, as well as various other immunogenic, metabolic, cytoskeletal and nuclear proteins. Post-translational deimination may facilitate protein moonlighting, an evolutionary conserved phenomenon, allowing one polypeptide chain to carry out various functions to meet functional requirements for diverse roles in immune defences and tissue remodelling.

Comparative Study of Immune Reaction Against Bacterial Infection From Transcriptome Analysis

Transcriptome analysis is a powerful tool that enables a deep understanding of complicated physiological pathways, including immune responses. RNA sequencing (RNA-Seq)-based transcriptome analysis and various bioinformatics tools have also been used to study non-model animals, including aquaculture species for which reference genomes are not available. Rapid developments in these techniques have not only accelerated investigations into the process of pathogenic infection and defense strategies in fish, but also used to identify immunity-related genes in fish. These findings will contribute to fish immunotherapy for the prevention and treatment of bacterial infections through the design of more specific and effective immune stimulants, adjuvants, and vaccines. Until now, there has been little information regarding the universality and diversity of immune reactions against pathogenic infection in fish. Therefore, one of the aims of this paper is to introduce the RNA-Seq technique for examination of immune responses in pathogen-infected fish. This review also aims to highlight comparative studies of immune responses against bacteria, based on our previous findings in largemouth bass (Micropterus salmoides) against Nocardia seriolae, gray mullet (Mugil cephalus) against Lactococcus garvieae, orange-spotted grouper (Epinephelus coioides) against Vibrio harveyi, and koi carp (Cyprinus carpio) against Aeromonas sobria, using RNA-seq techniques. We demonstrated that only 39 differentially expressed genes (DEGs) were present in all species. However, the number of specific DEGs in each species was relatively higher than that of common DEGs; 493 DEGs in largemouth bass against N. seriolae, 819 DEGs in mullets against L. garvieae, 909 in groupers against V. harveyi, and 1471 in carps against A. sobria. The DEGs in different fish species were also representative of specific immune-related pathways. The results of this study will enhance our understanding of the immune responses of fish, and will aid in the development of effective vaccines, therapies, and disease-resistant strains.

N-terminal domain of EcC1INH in Epinephelus coioides can antagonize the LPS-stimulated inflammatory response

Complement 1 inhibitor (C1INH) serving as a multifunctional factor can participate in the regulation of complement cascades and attenuate the activation of various proteases. In this study, we obtained EcC1INH cDNA and the tissue-specific analysis indicate that the highest expression level of EcC1INH mRNA was detected in liver. Moreover, Vibrio alginolyticus challenge can significantly increase EcC1INH mRNA expression in liver and kidney. N-terminal domain of EcC1INH could decrease LPS binding activity to cell surface, while loss of positively charged residues (PCRs) Arg21, His22, Lys50, Arg61 in N-terminal domain of EcC1INH can significantly reduce its interaction with LPS. Furthermore, LPS injection experiment indicated that the binding of EcC1INH N-terminal domain to LPS can antagonize LPS-induced inflammatory signaling pathway and attenuate the production of proinflammatory cytokines in vivo, indicating that EcC1INH was involved in negative regulation of inflammatory response.

Site-Specific N-Glycan Characterization of Grass Carp Serum IgM

Immunoglobulin M (IgM) is the major antibody in teleost fish and plays an important role in humoral adaptive immunity. The N-linked carbohydrates presenting on IgM have been well documented in higher vertebrates, but little is known regarding site-specific N-glycan characteristics in teleost IgM. In order to characterize these site-specific N-glycans, we conducted the first study of the N-glycans of each glycosylation site of the grass carp serum IgM. Among the four glycosylation sites, the Asn-262, Asn-303, and Asn-426 residues were efficiently glycosylated, while Asn-565 at the C-terminal tailpiece was incompletely occupied. A striking decrease in the level of occupancy at the Asn-565 glycosite was observed in dimeric IgM compared to that in monomeric IgM, and no glycan occupancy of Asn-565 was observed in tetrameric IgM. Glycopeptide analysis with liquid chromatography-electrospray ionization tandem mass spectrometry revealed mainly complex-type glycans with substantial heterogeneity, with neutral; monosialyl-, disialyl- and trisialylated; and fucosyl-and non-fucosyl-oligosaccharides conjugated to grass carp serum IgM. Glycan variation at a single site was greatest at the Asn-262 glycosite. Unlike IgMs in other species, only traces of complex-type and no high-mannose glycans were found at the Asn-565 glycosite. Matrix-assisted laser desorption ionization analysis of released glycans confirmed the overwhelming majority of carbohydrates were of the complex-type. These results indicate that grass carp serum IgM exhibits unique N-glycan features and highly processed oligosaccharides attached to individual glycosites.

Molecular cloning, characterization and expression analysis of complement components in red sea bream (Pagrus major) after Edwardsiella tarda and red sea bream Iridovirus (RSIV) challenge

The complement system plays an important role in immune regulation and acts as the first line of defense against any pathogenic attack. To comprehend the red sea bream (Pagrus major) immune response, three complement genes, namely, pmC1r, pmMASP and pmC3, belonging to the classical, lectin and alternative complement cascade, respectively, were identified and characterized. pmC1r, pmMASP, and pmC3 were comprised of 2535, 3352, and 5735 base mRNA which encodes 732, 1029 and 1677 aa putative proteins, respectively. Phylogenetically, all the three studied genes clustered with their corresponding homologous clade. Tissue distribution and cellular localization data demonstrated a very high prevalence of all the three genes in the liver. Both bacterial and viral infection resulted in significant transcriptional alterations in all three genes in the liver with respect to their vehicle control counterparts. Specifically, bacterial challenge affected the pmMASP and pmC3 expression, while the viral infection resulted in pmC1r and pmC3 mRNA activation. Altogether, our data demonstrate the ability of pmC1r, pmMASP and pmC3 in bringing about an immune response against any pathogenic encroachment, and thus activating, not only one, but all the three complement pathways, in red sea bream.

Specific humoral immunity in Osteichthyes

The fish immune system is extremely complex and has considerable adaptive potential. In Osteichthyes, the system is formed by lymphopoietic organs which are important for the differentiation and maturation of the immune system cells. These organs include the anterior kidney (phronephros), the thymus, the spleen, the posterior kidney (mesonephros), and mucosa-associated lymphoid tissues (MALT). Apart from the lymphocytic organs and the MALT system, the immune system components include defensive cells and their products. Those identified in fish include, inter alia, monocytes/macrophages, melanomacrophages, neutrophilic granulocytes, thrombocytes, B cells, plasma cells, and T cells. The roles of the individual components of the organisation of the immune system, the organs, and lymphoid tissue as well as the constituents conditioning the innate and adaptive immunity mechanisms are considered equally important, especially in the context of functional interdependence. The progress in the exploration of the processes of specific humoral immunity in Osteichthyes and the possibilities of their practical application is increasingly promising in view of the expected need for protection of fish against diseases.

The paper discusses selected issues concerning recent knowledge about haematopoiesis of B cells, plasmablasts, plasma cells, and immunoglobulins (IgM, IgD, IgT/IgZ).

High-throughput proteomic profiling of the fish liver following bacterial infection

Background

High-throughput proteomics was used to determine the role of the fish liver in defense responses to bacterial infection. This was done using a rainbow trout (Oncorhynchus mykiss) model following infection with Aeromonas salmonicida, the causative agent of furunculosis. The vertebrate liver has multifaceted functions in innate immunity, metabolism, and growth; we hypothesize this tissue serves a dual role in supporting host defense in parallel to metabolic adjustments that promote effective immune function. While past studies have reported mRNA responses to A. salmonicida in salmonids, the impact of bacterial infection on the liver proteome remains uncharacterized in fish.

Results

Rainbow trout were injected with A. salmonicida or PBS (control) and liver extracted 48 h later for analysis on a hybrid quadrupole-Orbitrap mass spectrometer. A label-free method was used for protein abundance profiling, which revealed a strong innate immune response along with evidence to support parallel rewiring of metabolic and growth systems. 3076 proteins were initially identified against all proteins (n = 71,293 RefSeq proteins) annotated in a single high-quality rainbow trout reference genome, of which 2433 were maintained for analysis post-quality filtering. Among the 2433 proteins, 109 showed significant differential abundance following A. salmonicida challenge, including many upregulated complement system and acute phase response proteins, in addition to molecules with putative functions that may support metabolic re-adjustments. We also identified novel expansions in the complement system due to gene and whole genome duplication events in salmonid evolutionary history, including eight C3 proteins showing differential changes in abundance.

Conclusions

This study provides the first high-throughput proteomic examination of the fish liver in response to bacterial challenge, revealing novel markers for the host defense response, and evidence of metabolic remodeling in conjunction with activation of innate immunity.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5092-0) contains supplementary material, which is available to authorized users.

Influences of Chlorella vulgaris dietary supplementation on growth performance, hematology, immune response and disease resistance in Oreochromis niloticus exposed to sub-lethal concentrations of penoxsulam herbicide

Little is known regarding the impact of penoxsulam, a fluorinated benzenesulfonamid rice herbicide, on Oreochromis niloticus (O. niloticus). Therefore, the current study was undertaken to highlight the effects of penoxsulam exposure on O. niloticus and to evaluate the advantages of Chlorella vulgaris (CV) dietary supplementation against the induced effects. The 96-h lethal concentration 50 (LC₅₀) penoxsulam value for O. niloticus was estimated at 8.948 mg/L by probit analysis in a static bioassay experiment. Next, 360 healthy fish were randomly allocated into 6 treatment groups. The T1 group served as the negative control and was fed a basal diet. The T2 group served as the positive control and was fed a basal diet supplemented with 10% CV. The fish in the T3 and T4 groups were exposed to 1/10 the 96-h LC₅₀ of penoxsulam (0.8948 mg/L) and were fed the basal diet alone or the basal diet supplemented with 10% CV, respectively. The fish in the T5 and T6 groups were exposed to 1/5 the 96-h LC₅₀ of penoxsulam (1.7896 mg/L) and fed the basal diet alone or the basal diet supplemented with 10% CV, respectively. Sub-acute penoxsulam exposure significantly altered hematological indices, as well as compromised the fish's immune defense mechanisms, including the phagocytic percentage, phagocytic index, nitric oxide production, immunoglobulin M levels and lysozyme, anti-trypsin and bactericidal activities subsequently decreasing O. niloticus's resistance to the Aeromonus sobria challenge and increasing disease symptoms and the mortality rate. Furthermore, sub-chronic penoxsulam exposure markedly altered growth performance, oxidant/antioxidant status and liver status and down-regulated the expression of interleukin-1β (IL-1β) and tumor necrosis-α (TNF-α). Interestingly, incorporating 10% CV into the diet protects fish against sub-acute penoxsulam-induced immunotoxicity via improvement of immune responses that increases the resistance against bacterial infection. Further, it improved the growth performance, oxidant/antioxidant status, liver status and markedly up-regulated immune-related gene expression, IL-1β and TNF-α, in the spleens of fish sub-chronically exposed to penoxsulam. These outcomes showed that dietary CV supplementation can protect the commercially valuable freshwater fish O. niloticus against penoxsulam toxicity and may be a potential feed supplement for Nile tilapia in aquaculture.

Effects of starch-coating of magnetite nanoparticles on cellular uptake, toxicity and gene expression profiles in adult zebrafish

Engineered magnetite nanoparticles (Fe₃O₄ NPs) have been used in many fields. To prevent particle agglomeration, stabilizers or coatings are often required. While such coatings have been shown to enhance performances, the environmental impact or toxicity of stabilized or coated Fe₃O₄ NPs remain poorly understood. In an effort to understand the impacts of such coatings on the toxicity of Fe₃O₄ NPs, we used the transcriptome sequencing (RNA-seq) technique to characterize the gill and liver transcriptomes from adult zebrafish when exposed to bare and starch-stabilized Fe₃O₄ NPs for 7days, demonstrating remarkable differences in gene expression profiles, also known as differentially expressed genes (DEGs) profiles, in both tissues. Bare Fe₃O₄ NPs exerted greater toxicity than starch-coated Fe₃O₄ NPs in gill; in contrast, starch-Fe₃O₄ NPs triggered more severe damage on liver, though both bare and stabilized NPs appeared to share similar regulatory mechanisms. Quantitative real-time polymerase chain reactions using six genes each for the two tissues verified the RNA-seq results. The surface coatings play an important role in determining the nanoparticle toxicity, which in turn modulate cell uptake and biological responses, consequently impacting the potential safety and efficacy of nanomaterials.

Fish Immunoglobulins

The B cell receptor and secreted antibody are at the nexus of humoral adaptive immunity. In this review, we summarize what is known of the immunoglobulin genes of jawed cartilaginous and bony fishes. We focus on what has been learned from genomic or cDNA sequence data, but where appropriate draw upon protein, immunization, affinity and structural studies. Work from major aquatic model organisms and less studied comparative species are both included to define what is the rule for an immunoglobulin isotype or taxonomic group and what exemplifies an exception.

Transcriptome Analysis of the Innate Immunity-Related Complement System in Spleen Tissue of Ctenopharyngodon idella Infected with Aeromonas hydrophila

The grass carp (Ctenopharyngodon idella) is an important commercial farmed herbivorous fish species in China, but is susceptible to Aeromonas hydrophila infections. In the present study, we performed de novo RNA-Seq sequencing of spleen tissue from specimens of a disease-resistant family, which were given intra-peritoneal injections containing PBS with or without a dose of A. hydrophila. The fish were sampled from the control group at 0 h, and from the experimental group at 4, 8, 12, 24, 48 and 72 h. 122.18 million clean reads were obtained from the normalized cDNA libraries; these were assembled into 425,260 contigs and then 191,795 transcripts. Of those, 52,668 transcripts were annotated with the NCBI Nr database, and 41,347 of the annotated transcripts were assigned into 90 functional groups. 20,569 unigenes were classified into six main categories, including 38 secondary KEGG pathways. 2,992 unigenes were used in the analysis of differentially expressed genes (DEGs). 89 of the putative DEGs were related to the immune system and 41 of them were involved in the complement and coagulation cascades pathway. This study provides insights into the complement and complement-related pathways involved in innate immunity, through expression profile analysis of the genomic resources in C. idella. We conclude that complement and complement-related genes play important roles during defense against A. hydrophila infection. The immune response is activated at 4 h after the bacterial injections, indicating that the complement pathways are activated at the early stage of bacterial infection. The study has improved our understanding of the immune response mechanisms in C. idella to bacterial pathogens.

Characterization of the gene encoding component C3 of the complement system from the spider Loxosceles laeta venom glands: Phylogenetic implications

A transcriptome analysis of the venom glands of the spider Loxosceles laeta, performed by our group, in a previous study (Fernandes-Pedrosa et al., 2008), revealed a transcript with a sequence similar to the human complement component C3. Here we present the analysis of this transcript. cDNA fragments encoding the C3 homologue (Lox-C3) were amplified from total RNA isolated from the venom glands of L. laeta by RACE-PCR. Lox-C3 is a 5178 bps cDNA sequence encoding a 190kDa protein, with a domain configuration similar to human C3. Multiple alignments of C3-like proteins revealed two processing sites, suggesting that Lox-C3 is composed of three chains. Furthermore, the amino acids consensus sequences for the thioester was found, in addition to putative sequences responsible for FB binding. The phylogenetic analysis showed that Lox-C3 belongs to the same group as two C3 isoforms from the spider Hasarius adansoni (Family Salcitidae), showing 53% homology with these. This is the first characterization of a Loxosceles cDNA sequence encoding a human C3 homologue, and this finding, together with our previous finding of the expression of a FB-like molecule, suggests that this spider species also has a complement system. This work will help to improve our understanding of the innate immune system in these spiders and the ancestral structure of C3.

Characterisation and expression analysis of two terminal complement components: C7 and C9 from large yellow croaker, Larimichthys crocea

The large yellow croaker Larimichthys crocea, as one of the most economically important marine fish in China and East Asian countries, are facing the fatal attraction of various pathogens in recent years. Elucidation of the organism immunomodulatory mechanism of croaker response to pathogen infection is essential for the disease control. In present study, we reported for the first time the molecular characterization and expression analysis of two terminal complement components (TCCs) of croaker, Lc-C7 and Lc-C9. These two structural conserved TCCs were detected in many tissues in adult healthy fish, with highest levels detected in liver. The transcriptional expression analysis of Lc-C7 and Lc-C9 at different developmental stages showed a continuous increase towards hatch, however the two TCCs mRNA were not detected at the unfertilized stage, hinting the origination of these two TCCs after fertilization. Rapid and drastic responses to Vibrio alginolyticus challenge were observed for Lc-C7 and Lc-C9, suggesting the involvement of component C7 and C9 in innate immune responses to pathogenic invasion in teleost fish. These findings could deepen our understanding about immunomodulatory mechanisms of croaker and shed a new light to the role of component system in teleostean immunomodulation.

Transcriptome analysis of the effect of Vibrio alginolyticus infection on the innate immunity-related complement pathway in Epinephelus coioides

Background

Orange-spotted grouper (Epinephelus coioides) with protogynous hermaphroditic features are one of the most economically important aquaculture species in Taiwan. However, larvae stage grouper are susceptible to infection by the bacterial pathogen Vibrio alginolyticus. To better understand the molecular mechanisms of the immune response to V. alginolyticus in Epinephelus coioides larvae, we used high-throughput deep sequencing technology to study the effect of infection on gene expression.

Results

A total of 114,851,002 reads were assembled, consisting of 9,687,355,560 nucleotides; these were further assembled into 209,082 contigs with a mean length of 372 bp. Gene ontology (GO) analysis of the transcriptome revealed 12 cellular component subcategories, 16 molecular function subcategories, and 42 biological process subcategories (P value <0.05). A total of 32664 Epinephelus coioides genes were mapped to the Kyoto Encyclopedia of Genes and Genomes (KEGG); 1504 differentially expressed genes (DEGs) were subsequently identified, in 12 categories (P value <0.05). Vibrio infection affected the expression of genes involved in complementation, coagulation cascades, pathogen (Staphylococcus aureus) infection, phagosome activity, antigen processing, and the antigen presentation pathway.

Conclusion

We conclude that the complement pathway of innate immunity and the hepicidin antimicrobial peptide may play important roles in the defense of Epinephelus coioides larvae against V. alginolyticus, and the immune response may activate at 4 h after bacterial infection. These results implicate the complement pathway signal pathway in immunity during V. alginolyticus infection at early developmental stages, enhancing our understanding of the mechanisms underlying the immune response to Vibrio infection in Epinephelus coioides.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-1102) contains supplementary material, which is available to authorized users.

Effects of changes in food supply at the time of sex differentiation on the gonadal transcriptome of juvenile fish. Implications for natural and farmed populations

Background

Food supply is a major factor influencing growth rates in animals. This has important implications for both natural and farmed fish populations, since food restriction may difficult reproduction. However, a study on the effects of food supply on the development of juvenile gonads has never been transcriptionally described in fish.

Methods and Findings

This study investigated the consequences of growth on gonadal transcriptome of European sea bass in: 1) 4-month-old sexually undifferentiated fish, comparing the gonads of fish with the highest vs. the lowest growth, to explore a possible link between transcriptome and future sex, and 2) testis from 11-month-old juveniles where growth had been manipulated through changes in food supply. The four groups used were: i) sustained fast growth, ii) sustained slow growth, iii) accelerated growth, iv) decelerated growth. The transcriptome of undifferentiated gonads was not drastically affected by initial natural differences in growth. Further, changes in the expression of genes associated with protein turnover were seen, favoring catabolism in slow-growing fish and anabolism in fast-growing fish. Moreover, while fast-growing fish took energy from glucose, as deduced from the pathways affected and the analysis of protein-protein interactions examined, in slow-growing fish lipid metabolism and gluconeogenesis was favored. Interestingly, the highest transcriptomic differences were found when forcing initially fast-growing fish to decelerate their growth, while accelerating growth of initially slow-growing fish resulted in full transcriptomic convergence with sustained fast-growing fish.

Conclusions

Food availability during sex differentiation shapes the juvenile testis transcriptome, as evidenced by adaptations to different energy balances. Remarkably, this occurs in absence of major histological changes in the testis. Thus, fish are able to recover transcriptionally their testes if they are provided with enough food supply during sex differentiation; however, an initial fast growth does not represent any advantage in terms of transcriptional fitness if later food becomes scarce.

Genomic characterization and expression pattern of Bf/C2 and C4 in miiuy croaker and molecular evolution analysis on mammals and fishes

The complement system plays an important role in both innate and adaptive host defense against the invading microorganisms in vertebrates. It can be activated by three pathways: the classical, alternative and lectin pathways. Bf/C2 and C4, as members of complement, play a pivotal role in the activation of the complement system. In our study, we identified Bf/C2 and C4 genes and genomic structure in miiuy croaker, and expression patterns of Bf/C2 and C4 genes was analyzed. In healthy miiuy croaker tissues, Bf/C2 and C4 genes were found to be ubiquitously expressed in all ten tested tissues. Analysis of expression of Bf/C2 and C4 genes after bacterial infection showed a significant up-regulated in liver. The evolutionary analysis showed that the ancestral lineages of Bf/C2 and C4 genes in mammals and fishes experienced positive selection indicated that the ancestors of mammals and fishes had further evolved to adapt to their environment, respectively. A series of maximum likelihood (ML) methods were used to study the evolution on vertebrates' Bf/C2 and C4 genes. One and five positive selection sites were found in mammals of Bf/C2 and C4 genes, but no positive selection site was found in fishes of Bf/C2 and C4 genes, indicating that Bf/C2 and C4 genes in mammals and fishes underwent different evolutionary patterns.

RNA-seq profiles from grass carp tissues after reovirus (GCRV) infection based on singular and modular enrichment analyses

Hemorrhagic disease of the grass carp, Ctenopharyngodon idella, is a fatal disease in fingerlings and yearlings caused by a reovirus, GCRV. RNA-seq data from four diseased grass carp tissues (gill, intestine, liver and spleen) were obtained at 2h before and six times after (2h, 24h, 48h, 72h, 96h and 120h) GCRV challenge. A total of 7.25±0.18 million (M) clean reads and 3.53±0.37M unique reads were obtained per RNA-seq analysis. Compared with controls, there were 9060 unique differentially expressed genes (DEGs) in the four tissues at the six time points post-GCRV challenge. Hierarchical clustering analysis of the DEGs showed that the data from the six time points fell into three branches: 2h, 24h/48h, and 72h/96h/120h. Singular (SEA) and modular enrichment analyses of DEGs per RNA-seq dataset were performed based on gene ontology. The results showed that immune responses occurred in all four tissues, indicating that GCRV probably does not target any tissue specifically. Moreover, during the course of disease, disturbances were observed in lipid and carbohydrate metabolism in each of the organs. SEA of DEGs based on the Kyoto Encyclopedia of Genes and Genomes database was also performed, and this indicated that the complement system and cellular immunity played an important role during the course of hemorrhagic disease. The qPCR of pooled samples of duplicate challenge experiment were used to confirm our RNA-seq approach.

The teleost humoral immune response

Over the past 10 years our knowledge of cellular and molecular dynamics of teleost humoral immunity has increased enormously to now include: the existence of multiple isotypes, affinity-driven modulation of antibody structure and function, the unique trafficking patterns of each stage of B cell differentiation (including the plasma blast, short-lived and long-lived plasma cell, and the memory cell). Unfortunately the work which has generated the bulk of this information has generally employed defined antigens rather than vaccines. Thus, the focus of this review is to relate these aspects of immunity that are requisite for a mechanistic understanding of the generation of prophylactic immunity to the necessary analysis of responses to vaccines and vaccine candidates.

The complement system in teleost fish: progress of post-homolog-hunting researches

Studies on the complement system of bony fish are now finishing a stage of homologue-hunting identification of the components, unveiling existence of almost all the orthologues of mammalian complement components in teleost. Genomic and transcriptomic data for several teleost species have contributed much for the homologue-hunting research progress. Only an exception is identification of orthologues of mammalian complement regulatory proteins and complement receptors. It is of particular interest that teleost complement components often exist as multiple isoforms with possible functional divergence. This review summarizes research progress of teleost complement system following the molecular identification and sequence analysis of the components. The findings of extensive expression analyses of the complement components with special emphasis of their prominent extrahepatic expression, acute-phase response to immunostimulation and various microbial infections, and ontogenic development including maternal transfer are discussed to infer teleost-specific functions of the complement system. Importance of the protein level characterization of the complement components is also emphasized, especially for understanding of the isotypic diversity of the components, a unique feature of teleost complement system.

Multiple tissue transcriptomic responses toPiscirickettsia salmonisin Atlantic salmon (Salmo salar)

The bacterium Piscirickettsia salmonis is the etiological agent of salmonid rickettsial septicemia (SRS), a severe disease that causes major economic losses to the Atlantic salmon aquaculture industry every year. Little is known about the infective strategy of P. salmonis, which is able to infect, survive within, and replicate inside salmonid macrophages as an intracellular parasite. Similarly there is little knowledge concerning the fish host's response to invasion by this pathogen. We have examined the transcriptional response of postsmolt Atlantic salmon ( Salmo salar) to P. salmonis at 48 h following infection in three tissues, liver, head kidney, and muscle, using an Atlantic salmon oligonucleotide microarray (Salar_2, Agilent 4x44K). The infection led to a large alteration of transcriptional activity in all the tissues studied. In infected salmon 886, 207, and 153 transcripts were differentially expressed in liver, head kidney, and muscle, respectively. Assessment of enrichment for particular biological pathways by gene ontology analysis showed an upregulation of genes involved in oxidative and inflammatory responses in infected fish, indicative of the activation of the innate immune response. The downregulation of genes involved in the adaptive immune response, G protein signaling pathway, and apoptotic process in infected fish may be reflective of mechanisms used by P. salmonis to survive, replicate, and escape host defenses. There was also evidence of differential responses between studied tissues, with protein metabolism being decreased in muscle of infected fish and with a concomitant increase being shown in liver.

Formulations combining CpG containing oliogonucleotides and poly I:C enhance the magnitude of immune responses and protection against pancreas disease in Atlantic salmon

Both CpG oligodeoxynucleotides and double-stranded RNA (poly I:C) have documented effects as treatments against several viral diseases in fish. However, as stand-alone treatments their effects have been modest. We have tested here whether CpG and poly I:C, alone or in combination induce protection against Salmonid Alphavirus (SAV), the causative agent of pancreas disease in Atlantic salmon. Our results revealed a significant reduction of viraemia 2 weeks after ip injection of the combined treatment and 1 week after challenge with SAV subtype 3, followed by reduced SAV induced heart pathology 3 weeks later. The SAV titers in blood samples from the combination group were lower as compared to single treatments with either CpG or poly I:C. Surprisingly, reduced SAV levels could also be found in fish as long as 7 weeks after receiving the combination treatment. The expression of IFNγ and to a lesser extent IFNa and Mx was up-regulated in head kidney and spleen 5 days after the fish had been treated with CpG and poly I:C. Furthermore, the complement factor C4 was depleted in serum 8 weeks post treatment, suggesting complement activation leading to C4 consumption. We hypothesize that the CpG/poly I:C-induced protection against SAV3 is mediated by mechanisms involving type I and type II IFN induced antiviral activity and complement mediated protective responses.

Transcriptomic responses to functional feeds in Atlantic salmon (Salmo salar)

Functional feeds are diets that have positive effects on both health and growth promoting performance of the animals ingesting them, by supplying additional compounds above and beyond the basic nutritional requirements for animal growth alone. The most common additives used in aquaculture diets are probiotics, prebiotics, immunostimulants, vitamins and nucleotides. Inclusion of these components to fish diets can increase feed conversion efficiency and growth, as well as having positive effects on the fish immune system. This review discusses the results from previous studies on fish nutrition and includes a novel genomic approach, using microarray analysis, to elucidate nutritional responses in Atlantic salmon (Salmo salar) fed a newly developed functional feed health premix diet. The transcriptome analysis demonstrated that compared to the standard diet feeding with the functional feed had significant effects on biological processes in the liver. This resulted in a reduction of the expression of genes related to protein turnover, reduced circulating plasma proteins and a down regulation of genes involved in the immune response. These results suggest that the functional feed may infer a decrease in whole body metabolic demands, suppressing both protein turnover and whole body oxygen demand, as well as down regulating several genes involved in the innate immune system. Together these changes appear to result in less energy wastage in fish and an enhanced growth and performance.

Starvation alters the liver transcriptome of the innate immune response in Atlantic salmon (Salmo salar)

BACKGROUND

The immune response is an energy demanding process, which has effects in many physiological pathways in the body including protein and lipid metabolism. During an inflammatory response the liver is required to produce high levels of acute phase response proteins that attempt to neutralise an invading pathogen. Although this has been extensively studied in both mammals and fish, little is known about how high and low energy reserves modulate the response to an infection in fish which are ectothermic vertebrates. Food withdrawal in fish causes a decrease in metabolic rate so as to preserve protein and lipid energy reserves, which occurs naturally during the life cycle of many salmonids. Here we investigated how the feeding or fasting of Atlantic salmon affected the transcriptional response in the liver to an acute bacterial infection.

RESULTS

Total liver RNA was extracted from four different groups of salmon. Two groups were fed or starved for 28 days. One of each of the fed or starved groups was then exposed to an acute bacterial infection. Twenty four hours later (day 29) the livers were isolated from all fish for RNA extraction. The transcriptional changes were examined by micro array analysis using a 17 K Atlantic salmon cDNA microarray. The expression profiling results showed major changes in gene transcription in each of the groups. Enrichment for particular biological pathways was examined by analysis of gene ontology. Those fish that were starved decreased immune gene transcription and reduced production of plasma protein genes, and upon infection there was a further decrease in genes encoding plasma proteins but a large increase in acute phase response proteins. The latter was greater in magnitude than in the fish that had been fed prior to infection. The expression of several genes that were found altered during microarray analysis was confirmed by real time PCR.

CONCLUSIONS

We demonstrate that both starvation and infection have profound effects on transcription in the liver of salmon. There was a significant effect on the transcriptional response to infection depending on the prior feeding regime of the fish. It is likely that the energy demands on protein synthesis for acute phase response proteins are relatively high in the starved fish which have reduced energy reserves. This has implications for dietary control of fish if an immune response is anticipated.

Genomic view of the evolution of the complement system

The recent accumulation of genomic information of many representative animals has made it possible to trace the evolution of the complement system based on the presence or absence of each complement gene in the analyzed genomes. Genome information from a few mammals, chicken, clawed frog, a few bony fish, sea squirt, fruit fly, nematoda and sea anemone indicate that bony fish and higher vertebrates share practically the same set of complement genes. This suggests that most of the gene duplications that played an essential role in establishing the mammalian complement system had occurred by the time of the teleost/mammalian divergence around 500 million years ago (MYA). Members of most complement gene families are also present in ascidians, although they do not show a one-to-one correspondence to their counterparts in higher vertebrates, indicating that the gene duplications of each gene family occurred independently in vertebrates and ascidians. The C3 and factor B genes, but probably not the other complement genes, are present in the genome of the cnidaria and some protostomes, indicating that the origin of the central part of the complement system was established more than 1,000 MYA.

Maternal transfer of complement components C3-1, C3-3, C3-4, C4, C5, C7, Bf, and Df to offspring in rainbow trout (Oncorhynchus mykiss)

Defense mechanisms in developing fish are poorly known but before maturation of lymphoid organs and immunocompetence, innate mechanisms are essential. The complement system represents a major part of innate immunity. Our main objective was to map the presence of complement components early in fish development. Rainbow trout eggs, embryos, and hatchlings were assayed for the onset and duration of C3-1, C3-3, C3-4, C4, C5, C7, factor B, and factor D transcription using real-time reverse transcription-polymerase chain reaction. In general, complement transcript levels increased steadily from day 28 postfertilization to hatch, followed by a decrease during yolk-sac resorption. All the complement proteins studied were found in unfertilized eggs. There was no correlation between the transcript and protein levels throughout the study period. Complement proteins appeared in the liver, kidney, and intestine between day 7 and 35 but not until day 77 in the heart. This study is the first to address the ontogeny of several complement components and represents the first evidence that maternal transfer of complement components, other than C3, occurs in teleost fish.

Characterization of serum complement activity of saltwater (Crocodylus porosus) and freshwater (Crocodylus johnstoni) crocodiles

We employed a spectroscopic assay, based on the hemolysis of sheep red blood cells (SRBCs), to assess the innate immune function of saltwater and freshwater crocodiles in vitro. Incubation of serum from freshwater and saltwater crocodiles with SRBCs resulted in concentration-dependent increases in SRBC hemolysis. The hemolytic activity occurred rapidly, with detectable activity within 2 min and maximum activity at 20 min. These activities, in both crocodilian species, were heat sensitive, unaffected by 20 mM methylamine, and completely inhibited by low concentrations of EDTA, suggesting that the alternative serum complement cascade is responsible for the observed effects. The hemolytic activities of the sera were inhibited by other chelators of divalent metal ions, such as phosphate and citrate. The inhibition of SRBC hemolysis by EDTA could be completely restored by the addition of 10 mM Ca2+ or Mg2+, but not Ba2+, Cu2+ or Fe2+, indicating specificity for these metal ions. The serum complement activities of both crocodilians were temperature-dependent, with peak activities occurring at 25-30 degrees C and reduced activities below 25 degrees C and above 35 degrees C.