The warm temperature acclimation protein Wap65 as an immune response gene: its duplicates are differentially regulated by temperature and bacterial infections

Temperature alters the oxidative and metabolic biomarkers and expression of environmental stress-related genes in chocolate mahseer (Neolissochilus hexagonolepis)

Long-term acclimation temperature effects on biomarkers of oxidative stress, metabolic stress, expression of heat shock proteins (Hsps), and warm-temperature acclimation related 65-kDa protein (Wap65) were evaluated in the threatened chocolate mahseer (Neolissochilus hexagonolepis). Fifteen-day-old larvae were acclimated to different water temperatures (15, 19, 23-control group, 27, and 31 °C) for 60 days prior to the sampling for quantification of mRNA, enzyme, nitric oxide, and malondialdehyde (MDA) content. Acclimation to 31 °C increased the basal mRNA level of glutathione S-transferase alpha 1 (GSTa1), and activities of catalase (CAT), glutathione reductase (GR), and GST enzymes and but downregulated the expression of superoxide dismutase 1 (SOD1) in the whole-body homogenate. Other antioxidant genes, i.e., CAT and GPx1a, were unaffected at 31 °C, and nitric oxide (NO) concentration was significantly lower. In contrast, fish acclimated to 15 °C showed an upregulated transcript level of all the antioxidant genes and no significant difference in the CAT, GR, and GST enzymes. Activities of the metabolic enzymes, aspartate transaminase (AST) and alanine transaminase (ALT), were significantly lower at 15 °C. The expression of Hsp47 was upregulated at both 15 and 31 °C groups, whereas Hsp70 was elevated at 27 and 31 °C groups. Wap65-1 transcription did not show significant variation in treatment groups compared to control. Fish in the high (31 °C) and low-temperature (15 °C) acclimation groups were capable of maintaining oxidative stress by modulating their antioxidant transcripts, enzymes, and Hsps.

Genomic organization and gene evolution of two warm temperature acclimation proteins (Wap65s) of Micropterus salmoides and their responses to temperature and bacterial/viral infections

Warm temperature acclimation-related 65-kDa proteins (Wap65s) are fish plasma acute-phase glycoproteins homologous to hemopexin with high affinity and clearance for heme. The study characterized Mswap65-1 and Mswap65-2 genes in Micropterus salmoides. Structural analysis showed MsWap65s contained conserved heme-binding sites. MsWap65-1 had a chloride-binding site similar to hemopexin, while MsWap65-2 had an additional calcium-binding site. Phylogenetic and Ka/Ks analysis showed that fish Wap65s were evolutionarily conserved and underwent strong purifying selection. Functional divergence analysis indicated that fish Wap65-2 retained the putative function of ancestral Wap65, while Wap65-1 underwent neofunctional differentiation. QPCR showed Mswap65s were predominantly expressed in liver, but prolonged hyperthermy inhibited Mswap65-2 expression. Mswap65-2 expression was up-regulated in liver and spleen after Nocardia seriolae infection, while Mswap65-1 was down-regulated. MsWap65-2 may be associated with pathogenesis and play potential role in pathogen resistance. LMBV infection resulted in both significant downregulation of Mswap65s were both significantly down-regulated, with differences observed between sexes. We speculated the immune system might suppress expression after viral infection. Exogenous rMsWap65s were prepared, and injection of rMsWap65s alleviated phenylhydrazine-induced hemolysis and inhibited increases in heme, complement C3 and inflammatory symptoms. Our results contribute to an advanced understanding of the functions and mechanisms of MsWap65s in stress resistance.

Identification and characterization of warm temperature acclimation proteins (Wap65s) in rainbow trout (Oncorhynchus mykiss)

Hemopexin is a vital glycoprotein for processing excessive iron in blood and functions as an iron scavenger in mammals. Teleosts however, unlike mammals, have two known hemopexin paralogs called warm temperature acclimation-related 65 kDa protein (Wap65-1 and Wap65-2, collectively termed Wap65s). Although Wap65s in rainbow trout have been considered notable biomarkers with significantly higher and/or lower expression under conditions of stress or disease, the individual roles, similarities and differences between the two paralogs are not well known. The aim of this study was to gain an understanding of the characteristics and functions of trout Wap65s from the perspective of iron-metabolism, physiological roles, and relevant immunological responses. The expression of Wap65-1 and -2 in this study was determined in the face of challenges by Aeromonas salmonicida, infectious hematopoietic necrosis virus (IHNV), and iron-dextran. Immuno-histochemistry (IHC) was employed to localize the major cell types for Wap65-2 expression, and trout leukocytes were isolated and incubated with LPS and OxLDL for comprehending the immunological characteristics of Wap65-2. We demonstrate that Wap65-1 is expressed only in the liver but Wap65-2 is systemically expressed in most organs and tissues. Interestingly, Wap65-1 expression was not significantly changed under A. salmonicida and iron-dextran administration, but was significantly decreased under IHNV. In contrast, Wap65-2 was up-regulated in all challenged groups, however with different expression patterns in the blood and liver. These results suggested that the two paralogs may participate in different biological roles. IHC showed that Wap65-2 antibody had high affinity for leukocyte-like cells, and macrophages but not lymphocytes significantly increased expression under LPS and OxLDL stimulation. These results support the conclusion that trout Wap65-2, not Wap65-1 may have conventional hemopexin functions such as reported in mammals including effects on iron metabolism, inflammation, and acute-phase protein.

Proteomics of sea bass skin-scales exposed to the emerging pollutant fluoxetine compared to estradiol

Teleost fish skin-scales are essential for protection and homeostasis and the largest tissue in direct contact with the environment, but their potential as early indicators of pollutant exposure are hampered by limited knowledge about this model. This study evaluated multi-level impacts of in vivo exposure of European sea bass to fluoxetine (FLX, a selective serotonin-reuptake inhibitor and an emerging pollutant) and 17β-estradiol (E2, a natural hormone and representative of diverse estrogenic endocrine-disrupting pollutants). Exposed fish had significantly increased circulating levels of FLX and its active metabolite nor-FLX that, in contrast to E2, did not have estrogenic effects on most fish plasma and scale indicators. Quantitative proteomics using SWATH-MS identified 985 proteins in the scale total proteome. 213 proteins were significantly modified 5 days after exposure to E2 or FLX and 31 were common to both treatments and responded in the same way. Common biological processes significantly affected by both treatments were protein turnover and cytoskeleton reorganization. E2 specifically up-regulated proteins related to protein production and degradation and down-regulated the cytoskeleton/extracellular matrix and innate immune proteins. FLX caused both up- and down-regulation of protein synthesis and energy metabolism. Multiple estrogen and serotonin receptor and transporter transcripts were altered in sea bass scales after E2 and/or FLX exposure, revealing complex disruptive effects in estrogen/serotonin responsiveness, which may account for the partially overlapping effects of E2 and FLX on the proteome. A large number (103) of FLX-specifically regulated proteins indicated numerous actions independent of estrogen signalling. This study provides the first quantitative proteome of the fish skin-scale barrier, elucidates routes of action and biochemical and molecular signatures of E2 or FLX-exposure and identifies potential physiological consequences and candidate biomarkers of pollutant exposure, for monitoring and risk assessment.

Serum amyloid A is a positive acute phase protein in Russian sturgeon challenged with Aeromonas hydrophila

The immune system of sturgeons, one of the most ancient and economically valuable fish worldwide, is poorly understood. The lack of molecular tools and data about infection biomarkers hinders the possibility to monitor sturgeon health during farming and detect infection outbreaks. To tackle this issue, we mined publicly available transcriptomic datasets and identified putative positive acute-phase proteins (APPs) of Russian sturgeons that could be induced by a bacterial infection and monitored using non-invasive methods. Teleost literature compelled us to focus on five promising candidates: hepcidin, a warm acclimation associated hemopexin, intelectin, serum amyloid A protein (SAA) and serotransferrin. Among them, SAA was the most upregulated protein at the mRNA level in the liver of sturgeons challenged with heat-inactivated or live Aeromonas hydrophila. To assess whether this upregulation yielded increasing SAA levels in circulation, we developed an in-house ELISA to quantify SAA levels in sturgeon serum. Circulating SAA rose upon bacterial challenge and positively correlated with hepatic saa expression. This is the first time serum SAA has been quantified in an Actinopterygii fish. Since APPs vary across different fish species, our work sheds light on sturgeon acute-phase response, revealing that SAA is a positive APP with potential value as infection biomarker.

Characterization of carp seminal plasma Wap65-2 and its participation in the testicular immune response and temperature acclimation

Two functionally distinct isoforms of warm-temperature acclimation related 65-kDa protein (Wap65-1 and Wap65-2) with a role in the immune response are present in fish. To our knowledge, contrary to Wap65-1, Wap65-2 has neither been isolated nor functionally characterized in carp especially in reproductive system. The aim of this study was to characterize Wap65-2 and ascertain its functions in immune response and temperature acclimation within reproductive system. Wap65-2 corresponded to one of the most abundant proteins in carp seminal plasma, with a high immunologic similarity to their counterparts in seminal plasma of other fish species and a wide tissue distribution, with predominant expression in the liver. The immunohistochemical localization of Wap65-2 to spermatogonia, Leydig cells, and the epithelium of blood vessels within the testis suggests its role in iron metabolism during spermatogenesis and maintenance of blood-testis barrier integrity. Wap65-2 secretion by the epithelial cells of the spermatic duct and its presence around spermatozoa suggests its involvement in the protection of spermatozoa against damage caused by heme released from erythrocytes following hemorrhage and inflammation. Our results revealed an isoform-specific response of Wap65 to temperature acclimation and Aeromonas salmonicida infection which alters blood-testis barrier integrity. Wap65-2 seems to be related to the immune response against bacteria, while Wap65-1 seems to be involved in temperature acclimation. This study expands the understanding of the mechanism of carp testicular immunity against bacterial challenge and temperature changes, in which Wap65-2 seems to be involved and highlights their potential usefulness as biomarkers of inflammation and temperature acclimation.

Genistein and estradiol have common and specific impacts on the sea bass (Dicentrarchus labrax) skin-scale barrier

Teleost fish scales play important roles in animal protection and homeostasis. They can be targeted by endogenous estrogens and by environmental estrogenic endocrine disruptors. The phytoestrogen genistein is ubiquitous in the environment and in aquaculture feeds and is a disruptor of estrogenic processes in vertebrates. To test genistein disrupting actions in teleost fish we used a minimally invasive approach by analysing scales plucked from the skin of sea bass (Dicentrarchus labrax). Genistein transactivated all three fish nuclear estrogen receptors and was most potent with the Esr2, had the highest efficacy with Esr1, but reached, in all cases, transactivation levels lower than those of estradiol. RNA-seq revealed 254 responsive genes in the sea bass scales transcriptome with an FDR < 0.05 and more than 2-fold change in expression, 1 or 5 days after acute exposure to estradiol or to genistein. 65 genes were specifically responsive to estradiol and 106 by genistein while 83 genes were responsive to both compounds. Estradiol specifically regulated genes of protein/matrix turnover and genistein affected sterol biosynthesis and regeneration, while innate immune responses were affected by both compounds. This comprehensive study revealed the impact on the fish scale transcriptome of estradiol and genistein, providing a solid background to further develop fish scales as a practical screening tool for endocrine disrupting chemicals in teleosts.

Deiminated proteins in extracellular vesicles and plasma of nurse shark (Ginglymostoma cirratum) - Novel insights into shark immunity

Peptidylarginine deiminases (PADs) are phylogenetically conserved calcium-dependent enzymes which post-translationally convert arginine into citrulline in target proteins in an irreversible manner, causing functional and structural changes in target proteins. Protein deimination causes generation of neo-epitopes, affects gene regulation and also allows for protein moonlighting. Extracellular vesicles are found in most body fluids and participate in cellular communication via transfer of cargo proteins and genetic material. In this study, post-translationally deiminated proteins and extracellular vesicles (EVs) are described for the first time in shark plasma. We report a poly-dispersed population of shark plasma EVs, positive for phylogenetically conserved EV-specific markers and characterised by TEM. In plasma, 6 deiminated proteins, including complement and immunoglobulin, were identified, whereof 3 proteins were found to be exported in plasma-derived EVs. A PAD homologue was identified in shark plasma by Western blotting and detected an expected 70 kDa size. Deiminated histone H3, a marker of neutrophil extracellular trap formation, was also detected in nurse shark plasma. This is the first report of deiminated proteins in plasma and EVs, highlighting a hitherto unrecognized post-translational modification in key immune proteins of innate and adaptive immunity in shark.

Analysis of agglutinants elicited by antiserum of channel catfish immunized with extracellular proteins of virulent Aeromonas hydrophila

Motile Aeromonas septicemia (MAS), caused by new virulent Aeromonas hydrophila (vAh) strains, has been one of the major diseases in channel catfish in recent years. Previous studies showed that channel catfish developed immunity against vAh infection after immunization with the pathogen's extracellular proteins (ECP). To understand the mechanisms associated with the immunity, anti-ECP fish serum (antiserum) was analyzed in this study. Our results revealed that the antiserum elicited agglutination of both ECP and cells of vAh. Five fish proteins were identified in ECP agglutinants, including two innate immunity associated proteins (serotransferrin and rhamnose-binding lectin), two immunoglobulin M (IgM) molecules (IgM heavy chain and light chain) and a constitutively-produced protein (warm temperature acclimation protein). More than 68 vAh proteins in ECP were recognized and caused to aggregate by IgM in the antiserum. IgM was isolated from vAh cell agglutinants and the native IgM was shown to form a tetramer that was responsible for bacterial agglutination. Immunoblotting analysis indicated that the isolated native IgM was able to recognize some proteins in ECP, such as aerolysin and hemolysin (in the form of a high molecular weight heterologous polymer). Gene expression analysis by quantitative PCR showed that fish immunized with vAh ECP had more transcripts of genes coding for IgM, serotransferrin and rhamnose binding lectin than mock-immunized fish. Both innate and antibody-mediated immune responses in serum and expressed genes contributed to fish immunity upon immunization with ECP. Results of this study shed light on the versatility of vAh antigens and catfish IgM, which would help identify specific antigens for vaccine development and antigen specific antibodies in catfish.

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.

Dietary Creatine Supplementation in Gilthead Seabream (Sparus aurata): Comparative Proteomics Analysis on Fish Allergens, Muscle Quality, and Liver

The quality of fish flesh depends on the skeletal muscle's energetic state and delaying energy depletion through diets supplementation could contribute to the preservation of muscle's quality traits and modulation of fish allergens. Food allergies represent a serious public health problem worldwide with fish being one of the top eight more allergenic foods. Parvalbumins, have been identified as the main fish allergen. In this study, we attempted to produce a low allergenic farmed fish with improved muscle quality in controlled artificial conditions by supplementing a commercial fish diet with different creatine percentages. The supplementation of fish diets with specific nutrients, aimed at reducing the expression of parvalbumin, can be considered of higher interest and beneficial in terms of food safety and human health. The effects of these supplemented diets on fish growth, physiological stress, fish muscle status, and parvalbumin modulation were investigated. Data from zootechnical parameters were used to evaluate fish growth, food conversion ratios and hepatosomatic index. Physiological stress responses were assessed by measuring cortisol releases and muscle quality analyzed by rigor mortis and pH. Parvalbumin, creatine, and glycogen concentrations in muscle were also determined. Comparative proteomics was used to look into changes in muscle and liver tissues at protein level. Our results suggest that the supplementation of commercial fish diets with creatine does not affect farmed fish productivity parameters, or either muscle quality. Additionally, the effect of higher concentrations of creatine supplementation revealed a minor influence in fish physiological welfare. Differences at the proteome level were detected among fish fed with different diets. Differential muscle proteins expression was identified as tropomyosins, beta enolase, and creatine kinase among others, whether in liver several proteins involved in the immune system, cellular processes, stress, and inflammation response were modulated. Regarding parvalbumin modulation, the tested creatine percentages added to the commercial diet had also no effect in the expression of this protein. The use of proteomics tools showed to be sensitive to infer about changes of the underlying molecular mechanisms regarding fish responses to external stimulus, providing a holistic and unbiased view on fish allergens and muscle quality.

Identification of warm temperature acclimation-associated 65-kDa protein-2 in Kumgang fat minnow Rhynchocypris kumgangensis

Warm temperature acclimation-associated 65-kDa protein (Wap65) is known to respond to elevated water temperatures and the corresponding gene from several fish species has been cloned. Expression of Wap65 gene is induced by various physiological stresses, such as increase in water temperature, immune response and heavy metal exposure. Two isolated Wap65 genes, Wap65-1 and Wap65-2, display distinct tissue distribution and physiological functions despite high sequence homology. In a previous study, we identified the Wap65-1 gene (kmWap65-1) from Kumgang fat minnow, Rhynchocypris kumgangensis, a small freshwater fish endemic to Korea. The kmWap65-1 gene showed sequence homology with teleost Wap65-1 and mammalian hemopexin, and was highly expressed in response to increased water temperature and bacterial lipopolysaccharide (LPS) exposure. Here, we isolated kmWap65-2 from liver tissue of Kumgang fat minnow and compared the expression profiles of both kmWap65 genes following exposure to various physiological stresses, including thermal changes, bacterial challenge, and environmental toxins. Notably, while kmWap65-1 expression was significantly increased in response to high water temperature, LPS, cadmium, and iron, kmWap65-2 displayed no alterations in expression at high water temperature. However, kmWap65-2 expression was upregulated slightly in response to LPS and highly in presence of copper, bisphenol A, and estradiol. Based on the collective findings, we propose that kmWap65-1 and kmWap65-2 are multifunctional proteins with distinct functions that could serve as useful biomarkers for assessing physiological stress and associated responses in Kumgang fat minnow.

Hypothermal stress induced differential expression profiles of the immune response gene, warm-temperature-acclimation associated 65-kDa protein (Wap65), in the liver of fresh water and seawater milkfish, Chanos chanos

The milkfish (Chanos chanos), an important aquaculture species, is intolerant to cold environments. Temperature fluctuations in the environment affect the physiological response, behavior, and survival rate of the fish. The warm-temperature-acclimation associated 65-kDa protein (Wap65) of teleosts was identified after heat shock treatment and has two isoforms. Both the isoforms were involved in the induction of immune responses in fish. They showed high degree of sequence conservation with the mammalian hemopexin and had high affinity for heme, which helped in the neutralization of free-heme and its transport to the liver. In this study, we isolated and characterized the two isoforms of wap65 genes (Ccwap65-1 and Ccwap65-2) from the liver of milkfish. The Ccwap65-1 and Ccwap65-2 are mainly expressed in livers of milkfish. In hypothermal treatment, the expression levels of Ccwap65-2 in the livers of SW and FW milkfish were up-regulated after exposure to low temperature (18 °C) for 12 h and 96 h compared to those in the normal temperature (28 °C) group, respectively. After intraperitoneal injection of lipopolysaccharide (LPS), the expression of Ccwap65-2 was elevated in both SW and FW milkfish, whereas that of Ccwap65-1 was not affected in both the groups. Thus, Ccwap65-2 expressed in the milkfish liver under hypothermal stress was identified as a novel immune biomarker. In addition, according to the transcriptome database, up-regulation of the other immune-response genes indicated increased pathogen infection status under hypothermal stress. Acute increase in the expression of hepatic Ccwap65-2 in response to pathogen infection might lead to better cold tolerance of SW milkfish compared to that of the FW individuals upon cold challenge.

Nutritional Immunity Triggers the Modulation of Iron Metabolism Genes in the Sub-Antarctic Notothenioid Eleginops maclovinus in Response to Piscirickettsia salmonis

Iron deprivation is a nutritional immunity mechanism through which fish can limit the amount of iron available to invading bacteria. The aim of this study was to evaluate the modulation of iron metabolism genes in the liver and brain of sub-Antarctic notothenioid Eleginops maclovinus challenged with Piscirickettsia salmonis. The specimens were inoculated with two P. salmonis strains: LF-89 (ATCC^® VR-1361™) and Austral-005 (antibiotic resistant). Hepatic and brain samples were collected at intervals over a period of 35 days. Gene expression (by RT-qPCR) of proteins involved in iron storage, transport, and binding were statistically modulated in infected fish when compared with control counterparts. Specifically, the expression profiles of the transferrin and hemopexin genes in the liver, as well as the expression profiles of ferritin-M, ferritin-L, and transferrin in the brain, were similar for both experimental groups. Nevertheless, the remaining genes such as ferritin-H, ceruloplasmin, hepcidin, and haptoglobin presented tissue-specific expression profiles that varied in relation to the injected bacterial strain and sampling time-point. These results suggest that nutritional immunity could be an important immune defense mechanism for E. maclovinus against P. salmonis injection. This study provides relevant information for understanding iron metabolism of a sub-Antarctic notothenioid fish.

Skin mucus proteins of lumpsucker (Cyclopterus lumpus)

Fish skin mucus serves as a first line of defense against pathogens and external stressors. In this study the proteomic profile of lumpsucker skin mucus was characterized using 2D gels coupled with tandem mass spectrometry. Mucosal proteins were identified by homology searches across the databases SwissProt, NCBInr and vertebrate EST. The identified proteins were clustered into ten groups based on their gene ontology biological process in PANTHER (www.patherdb.org). Calmodulin, cystatin-B, histone H2B, peroxiredoxin1, apolipoprotein A1, natterin-2, 14-3-3 protein, alfa enolase, pentraxin, warm temperature acclimation 65 kDa (WAP65kDa) and heat shock proteins were identified. Several of the proteins are known to be involved in immune and/or stress responses. Proteomic profile established in this study could be a benchmark for differential proteomics studies.

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A proteome reference map of lumpsucker skin mucus was established.

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Proteins involved in immune and stress responses were identified in skin mucus of Cyclopterus lumpus.

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Mucosal proteins identified could be potential biomarkers.

Identification of a warm-temperature acclimation-associated 65-kDa protein encoded by a temperature- and infection-responsive gene in the Kumgang fat minnow Rhynchocypris kumgangensis

Water temperature is one of the most important factors in fish physiology; thus, it is important to identify genes that respond to changes in water temperature. In this study, we identified a warm- temperature acclimation-associated 65-kDa protein (Wap65) in the Kumgang fat minnow Rhynchocypris kumgangensis, a small, cold-freshwater fish species endemic to Korea. Kumgang fat minnow Wap65-1 (kmWap65-1) was cloned using polymerase chain reaction (PCR)-based strategies, and was found to be highly homologous with teleost Wap65-1 and mammalian hemopexin, a heme-binding protein that transfers plasma heme into hepatocytes. kmWap65-1 mRNA was expressed mainly in the liver and its expression levels were significantly increased by both short- and long-term exposure to high temperature, which was evaluated by real-time quantitative PCR. Furthermore, the expression levels of kmWap65-1 were highly elevated by exposure to bacterial lipopolysaccharide. These results indicate that kmWap65-1 expression is associated with environmental stresses such as increases in water temperature and bacterial infection. J. Exp. Zool. 325A:65-74, 2016. © 2015 Wiley Periodicals, Inc.

Skin mucus proteome map of European sea bass (Dicentrarchus labrax)

Skin mucus is the first barrier of fish defence. Proteins from skin mucus of European sea bass (Dicentrarchus labrax) were identified by 2DE followed by LC-MS/MS. From all the identified proteins in the proteome map, we focus on the proteins associated with several immune pathways in fish. Furthermore, the real-time PCR transcript levels in skin are shown. Proteins found include apolipoprotein A1, calmodulin, complement C3, fucose-binding lectin, lysozyme and several caspases. To our knowledge, this is the first skin mucus proteome study and further transcriptional profiling of the identified proteins done on this bony fish species. This not only contributes knowledge on the routes involved in mucosal innate immunity, but also establishes a non-invasive technique based on locating immune markers with a potential use for prevention and/or diagnosis of fish diseases.

Skin mucus proteome of gilthead sea bream: A non-invasive method to screen for welfare indicators

In teleosts, the skin mucus is the first physical barrier against physical and chemical attacks. It contains components related to metabolism, environmental influences and nutritional status. Here, we study mucus and composition based on a proteome map of soluble epidermal mucus proteins obtained by 2D-electrophoresis in gilthead sea bream, Sparus aurata. Over 1300 spots were recorded and the 100 most abundant were further analysed by LC-MS/MS and identified by database retrieval; we also established the related specific biological processes by Gene Ontology enrichment. Sixty-two different proteins were identified and classified in 12 GO-groups and into three main functions: structural, metabolic and protection-related. Several of the proteins can be used as targets to determine fish physiological status: actins and keratins, and especially their catabolic products, in the structural functional group; glycolytic enzymes and ubiquitin/proteasome-related proteins in the metabolic functional group; and heat shock proteins, transferrin and hemopexins, in the protection-related group. This study analyses fish mucus, a potential non-invasive tool for characterising fish status, beyond defence capacities, and we postulate some putative candidates for future studies along similar lines.

Differential gene expression in the liver of the African lungfish, Protopterus annectens, after 6 months of aestivation in air or 1 day of arousal from 6 months of aestivation

The African lungfish, Protopterus annectens, can undergo aestivation during drought. Aestivation has three phases: induction, maintenance and arousal. The objective of this study was to examine the differential gene expression in the liver of P. annectens after 6 months (the maintenance phase) of aestivation as compared with the freshwater control, or after 1 day of arousal from 6 months aestivation as compared with 6 months of aestivation using suppression subtractive hybridization. During the maintenance phase of aestivation, the mRNA expression of argininosuccinate synthetase 1 and carbamoyl phosphate synthetase III were up-regulated, indicating an increase in the ornithine-urea cycle capacity to detoxify ammonia to urea. There was also an increase in the expression of betaine homocysteine-S-transferase 1 which could reduce and prevent the accumulation of hepatic homocysteine. On the other hand, the down-regulation of superoxide dismutase 1 expression could signify a decrease in ROS production during the maintenance phase of aestivation. In addition, the maintenance phase was marked by decreases in expressions of genes related to blood coagulation, complement fixation and iron and copper metabolism, which could be strategies used to prevent thrombosis and to conserve energy. Unlike the maintenance phase of aestivation, there were increases in expressions of genes related to nitrogen, carbohydrate and lipid metabolism and fatty acid transport after 1 day of arousal from 6 months aestivation. There were also up-regulation in expressions of genes that were involved in the electron transport system and ATP synthesis, indicating a greater demand for metabolic energy during arousal. Overall, our results signify the importance of sustaining a low rate of waste production and conservation of energy store during the maintenance phase, and the dependence on internal energy store for repair and structural modification during the arousal phase, of aestivation in the liver of P. annectens.

Effect of size and temperature at vaccination on immunization and protection conferred by a live attenuated Francisella noatunensis immersion vaccine in red hybrid tilapia

Francisella noatunensis subsp. orientalis (Fno) is a pleomorphic, facultative intracellular, Gram-negative, emerging bacterial pathogen of marine and fresh water fish with worldwide distribution. In this study, the efficacy of an attenuated Fno intracellular growth locus C (iglC) mutant was evaluated for use as a live immersion vaccine, when administered to hybrid tilapia at two different stages of growth (5 g fry and 10 g fingerlings) and at two temperatures (25 °C and 30 °C). To determine vaccine efficacy, mortality, days to first death, and Fno genome equivalents (GE) in the spleens of survivors, as well as serum and mucus antibody levels, were evaluated after 30 d in fish challenged with a wild type virulent strain. Both size and temperature at vaccination played an important role in immunization and protection. Fry vaccinated at 25 °C were not protected when compared to non-vaccinated fry at 25 °C (p = 0.870). In contrast, 5 g fry vaccinated at 30 °C were significantly protected compared to non-vaccinated fry at 30 °C (p = 0.038). Although lower mortalities occurred, 10 g fingerlings vaccinated at 25 °C were not protected, compared to non-vaccinated fingerlings at 25 °C (p = 0.328), while, 10 g fingerlings vaccinated at 30 °C were significantly protected, compared to non-vaccinated fingerlings at 30 °C (p = 0.038). Additionally, overall mortality of 5 g fish was significantly higher than in 10 g fish. Mortality was also significantly higher in fish subjected to a 30 to 25 °C temperature change one week prior to challenge, than in fish maintained at the same temperature during vaccination and challenge. This information demonstrates that both temperature and size at vaccination are important factors when implementing immunization prophylaxis in cultured tilapia.

The warm temperature acclimation protein (Wap65) has an important role in the inflammatory response of turbot (Scophthalmus maximus)

Wap65 is a molecule similar to the mammalian hemopexin that is a serum glycoprotein produced mainly by the liver with high affinity to heme. Its primary role is participating in iron metabolism scavenging heme that is released into the plasma and transporting it to the liver. It has been reported an important role of hemopexin in the inflammation as an acute-phase protein and its production is up-regulated by pro-inflammatory cytokines. There are also some evidences suggesting this immune-induction in fish Wap65 genes. Most teleost species presents two Wap65 genes but their physiological functions have not been completely elucidated; in fact, the transcriptional patterns of Wap65 genes to stimulatory treatments are variable and contradictory. In the present study two Wap65 genes, Wap65-1 and Wap65-2, have been characterized for the first time in turbot (Scophthalmus maximus). Their constitutive expression and differential modulation by thermal treatments, immune challenges (bacterial and viral), as well as iron supplementation, have been investigated. Both genes were mainly expressed in liver, but they were detected in all tested tissues. Whereas Wap65-1 and Wap65-2 were up-regulated by temperature rise and bacterial challenge, VHSV infection inhibited the expression of both genes. Moreover, iron-dextran administration induced only the overexpression of Wap65-1. Interestingly, these induction were observed in head kidney buy not in liver. The effect of Wap65 protein purified from turbot serum by hemin-agarose affinity chromatography was also studied to demonstrate a possible anti-inflammatory role, analyzing its inhibitory effect on leucocytes migration induced by zymosan injection to the peritoneal cavity.

Impact of three commercial feed formulations on farmed gilthead sea bream (Sparus aurata, L.) metabolism as inferred from liver and blood serum proteomics

Background

The zootechnical performance of three different commercial feeds and their impact on liver and serum proteins of gilthead sea bream (Sparus aurata, L.) were assessed in a 12 week feeding trial. The three feeds, named A, B, and C, were subjected to lipid and protein characterization by gas chromatography (GC) and liquid chromatography-tandem mass spectrometry (LC-MS/MS), respectively.

Results

Feed B was higher in fish-derived lipids and proteins, while feeds C and A were higher in vegetable components, although the largest proportion of feed C proteins was represented by pig hemoglobin. According to biometric measurements, the feeds had significantly different impacts on fish growth, producing a higher average weight gain and a lower liver somatic index in feed B over feeds A and C, respectively. 2D DIGE/MS analysis of liver tissue and Ingenuity pathways analysis (IPA) highlighted differential changes in proteins involved in key metabolic pathways of liver, spanning carbohydrate, lipid, protein, and oxidative metabolism. In addition, serum proteomics revealed interesting changes in apolipoproteins, transferrin, warm temperature acclimation-related 65 kDa protein (Wap65), fibrinogen, F-type lectin, and alpha-1-antitrypsin.

Conclusions

This study highlights the contribution of proteomics for understanding and improving the metabolic compatibility of feeds for marine aquaculture, and opens new perspectives for its monitoring with serological tests.

Electronic supplementary material

The online version of this article (doi:10.1186/s12953-014-0044-3) contains supplementary material, which is available to authorized users.

Genomic organization and functional diversification of two warm-temperature-acclimation-associated 65-kDa protein genes in rockbream (Oplegnathus fasciatus; Perciformes)

Two paralogue genes of warm-temperature-acclimation-associated 65-kDa protein were characterized and their mRNA expression patterns during various experimental stimulations were examined in the rockbream (Oplegnathus fasciatus; Perciformes). Rockbream Wap65 isoforms (rbWap65-1 and rbWap65-2) share basically common structural features with other teleostean orthologues and human hemopexin (HPX) at both amino acid (conserved cysteine and histidine residues) and genomic levels (ten-exon structure), although the rbWap65-2 reveals more homologous characteristics to human HPX than does rbWap65-1 isoform. Southern blot analysis indicates that each rbWap65 isoform exists as a single copy gene in the rockbream genome. Both rbWap65 genes were predicted to possess various transcription factor (TF) binding motifs related with stress and innate immunity in their 5ʹ-upstream regions, in which inflammation-related motifs were more highlighted in the rbWap65-2 than in rbWap65-1. Based on the RT-PCR assay, the liver-predominant expression pattern was more apparent in rbWap65-1 than rbWap65-2 isoform. During thermal elevation, clear upregulation was found only for the rbWap65-1. In contrast, immune stimulations (bacterial challenges, viral infection and iron overload) activated more preferentially the rbWap65-2 isoform in overall, although the inducibility was affected by the kinds of stimulators and tissue types. Taken together, our data suggest that the two paralogue rbWap65 isoforms have experienced subfunctionalization and/or neofunctionalization during their evolutionary history, in which the rbWap65-2 has retained closer, functional orthology to the human HPX while the rbWap65-1 have been diversified to be more related with thermal acclimation physiology.

Adaptive functional divergence of the warm temperature acclimation-related protein (WAP65) in fishes and the ortholog hemopexin (HPX) in mammals

Gene duplication is an important mechanism that leads to genetic novelty. Different, nonexclusive processes are likely involved, and many adaptive and nonadaptive events may contribute to the maintenance of duplicated genes. In some teleosts, a duplicate copy of the mammalian ortholog Hemopexin (HPX) is present, known as the warm temperature acclimation-related protein (WAP65). Both WAP65 and HPX have been associated with iron homeostasis due to the affinity to bind the toxic-free heme circulating in the blood stream. We have assessed the evolutionary dynamics of WAP65 and HPX genes to understand the adaptive role of positive selection at both nucleotide and amino acid level. Our results showed an asymmetrical evolution between the paralogs WAP65-1 and WAP65-2 after duplication with a slight acceleration of the evolutionary rate in WAP65-1, but not in WAP65-2, and few sites contributing to the functional distinction between the paralogs, whereas the majority of the protein remained under negative selection or relaxed negative selection. WAP65-1 is functionally more distinct from the ancestral protein function than WAP65-2. HPX is phylogenetically closer to WAP65-2 but even so functional divergence was detected between both proteins. In addition, HPX showed a fast rate of evolution when compared with both WAP65-1 and WAP65-2 genes. The assessed 3-dimensional (3-D) structure of WAP65-1 and WAP65-2 suggests that the functional differences detected are not causing noticeable structural changes in these proteins. However, such subtle changes between WAP65 paralogs may be important to understand the differential gene retention of both copies in 20 out of 30 teleosts species studied.

Proteomic approach to skin regeneration in a marine teleost: modulation by oestradiol-17β

Skin and scale formation and regeneration in teleosts have mainly been described from a morphological perspective, and few studies of the underlying molecular events exist. The present study evaluates (1) the change in the skin proteome during its regeneration in a marine teleost fish (gilthead sea bream, Sparus aurata) and (2) the impact of oestradiol-17β (Ε2) on regeneration and the involvement of oestrogen receptor (ER) isoforms. Thirty-five candidate proteins were differentially expressed (p < 0.05) between intact and regenerated skin proteome 5 days after scale removal, and 27 proteins were differentially expressed after E2 treatment. Agglomerative hierarchical clustering of the skin proteome revealed that the skin treated with E2 clustered most closely to intact skin, while regenerating untreated skin formed an independent cluster. Gene Ontology classification associated the differentially expressed proteins in E2-treated skin with developmental processes and cellular morphogenesis. The proteins modified during skin regeneration suggest a balance exists between immune response and anatomical repair. Overall, the results indicate that, even after 5 days regeneration, the composition of mature skin is not attained, and endocrine factors, in particular E2, can accelerate wound repair acting possibly via ERβs expressed in the skin-scales. Several candidate proteins probably involved in scale development, osteoglycin, lipocalin2 and lamin A and the transcription factors PHD and grainyhead were identified. Future studies of fish skin regeneration will be required to provide further insight into this multistage process, and the present study indicates it will be useful to explore immune adaptations of epithelia permanently exposed to an aqueous environment.

Genetic organization of two types of flounder warm-temperature acclimation-associated 65-kDa protein and their gene expression profiles

We isolated and characterized two cDNA clone encoding warm-temperature acclimation-associated 65-kDa proteins (PoWap65-1 and PoWap65-2) from the olive flounder, Paralichthys olivaceus. The deduced amino acid sequences of PoWap65s showed overall identities of 33-73% with other fish Wap65 and mammalian hemopexin-like proteins. The 5'-flanking regions of both PoWap65-encoding genes contained various putative transcriptional elements. While PoWap65-1 and PoWap65-2 were structurally similar, they exhibited highly differential patterns of expression. PoWap65-1 was expressed only in the liver, whereas PoWap65-2 transcripts were detected in a wide range of tissues. The accumulation of PoWap65s mRNA was expressed differentially during development. Expression of them in warm temperatures also differed in flounder embryonic cells. PoWap65-1 was upregulated by temperature stimulation whereas PoWap65-2 was not detected. PoWap65s were highly regulated by Edwardsiella tarda infection and hypoxia. Pathogen challenge induced PoWap65-2 expression in the liver whereas PoWap65-1 was downregulated. Hypoxia induced the expression of both PoWap65s in the liver of juvenile fish.

Four lysozymes (one c-type and three g-type) in catfish are drastically but differentially induced after bacterial infection

Lysozyme is an important component of the innate immune system. In this study, four lysozyme genes including one c-type lysozyme and three g-type lysozymes were identified from channel catfish (Ictalurus punctatus). The lysozyme genes are highly conserved in their structural features as compared to those from other species. Phylogenetic analyses were conducted allowing annotation of these genes. Additional analyses using conserved syntenies allowed determination of orthologies for the c-type lysozyme. Phylogenetic analysis indicated that the g-type lysozyme may have gone through species-specific gene duplications leading to multiple copies in some teleost species. Channel catfish possessed three copies of the g-type lysozyme genes. Expression analysis revealed that the catfish lysozyme genes were expressed in a broad range of tissues. The highest levels of expression were found in head kidney, liver, spleen, and trunk kidney, compatible with the immune functions of these tissues/organs. The c-type and g-type lysozymes were drastically induced after bacterial infection, but exhibited large differences in the extent of induction and the tissue with the highest level of induction, with the g-type lysozyme being most highly induced in the head kidney whereas the other three lysozymes being most highly induced in the liver, suggesting their cooperative actions in the immune responses but difference in their detailed functions.

Transcriptome sequencing and analysis of wild Amur Ide (Leuciscus waleckii) inhabiting an extreme alkaline-saline lake reveals insights into stress adaptation

Background

Amur ide (Leuciscus waleckii) is an economically and ecologically important species in Northern Asia. The Dali Nor population inhabiting Dali Nor Lake, a typical saline-alkaline lake in Inner Mongolia, is well-known for its adaptation to extremely high alkalinity. Genome information is needed for conservation and aquaculture purposes, as well as to gain further understanding into the genetics of stress tolerance. The objective of the study is to sequence the transcriptome and obtain a well-assembled transcriptome of Amur ide.

Results

The transcriptome of Amur ide was sequenced using the Illumina platform and assembled into 53,632 cDNA contigs, with an average length of 647 bp and a N50 length of 1,094 bp. A total of 19,338 unique proteins were identified, and gene ontology and KEGG (Kyoto Encyclopedia of Genes and Genomes) analyses classified all contigs into functional categories. Open Reading Frames (ORFs) were detected from 34,888 (65.1%) of contigs with an average length of 577 bp, while 9,638 full-length cDNAs were identified. Comparative analyses revealed that 31,790 (59.3%) contigs have a significant similarity to zebrafish proteins, and 27,096 (50.5%), 27,524 (51.3%) and 27,996 (52.2%) to teraodon, medaka and three-spined stickleback proteins, respectively. A total of 10,395 microsatellites and 34,299 SNPs were identified and classified. A dN/dS analysis on unigenes was performed, which identified that 61 of the genes were under strong positive selection. Most of the genes are associated with stress adaptation and immunity, suggesting that the extreme alkaline-saline environment resulted in fast evolution of certain genes.

Conclusions

The transcriptome of Amur ide had been deeply sequenced, assembled and characterized, providing a valuable resource for a better understanding of the Amur ide genome. The transcriptome data will facilitate future functional studies on the Amur ide genome, as well as provide insight into potential mechanisms for adaptation to an extreme alkaline-saline environment.

Molecular cloning, characterization and expression analysis of a novel wap65-1 gene from Plecoglossus altivelis

Warm temperature acclimation associated 65-kDa protein 1 (WAP65-1) is a specific fish plasma glycoprotein that is possibly involved in various physiological or pathological processes. In this study, we obtained the cDNA and genomic DNA sequences of the Plecoglossus altivelis wap65-1 (Pawap65-1) gene. Multiple sequence alignment showed that Pawap65-1 is similar in structure to wap65-1 in fish. Phylogenetic analysis revealed that Pawap65-1 is most closely related to that of a rainbow trout. Pawap65-1 transcripts are present in various tissues and are most abundant in the liver. We expressed recombinant PaWAP65-1 in Escherichia coli and raised antiserum against it in mouse. Western blot analysis revealed that the higher molecular mass of PaWAP65-1 in blood plasma was caused by post-translational N-glycosylation. Quantitative real-time quantitative PCR (qPCR) and Western blot analysis data showed that the hepatic mRNA and blood plasma levels of PaWAP65-1 were both influenced by warm temperature acclimation and cadmium exposure, but not by Listonella anguillarum infection, hypo-osmotic, or cold temperature acclimation. In conclusion, our data reveals that PaWAP65-1 is a stress-related protein, and may play a role in fish acclimation to warm temperature and cadmium exposure.

The innate immune-related genes in catfish

Catfish is one of the most important aquaculture species in America (as well as in Asia and Africa). In recent years, the production of catfish has suffered massive financial losses due to pathogen spread and breakouts. Innate immunity plays a crucial role in increasing resistance to pathogenic organisms and has generated increasing interest in the past few years. This review summarizes the current understanding of innate immune-related genes in catfish, including pattern recognition receptors, antimicrobial peptides, complements, lectins, cytokines, transferrin and gene expression profiling using microarrays and next generation sequencing technologies. This review will benefit the understanding of innate immune system in catfish and further efforts in studying the innate immune-related genes in fish.

Physiological and proteomic responses to single and repeated hypoxia in juvenile Eurasian perch under domestication--clues to physiological acclimation and humoral immune modulations

We evaluated the physiological and humoral immune responses of Eurasian perch submitted to 4-h hypoxia in either single or repeated way. Two generations (F1 and F5) were tested to study the potential changes in these responses with domestication. In both generations, single and repeated hypoxia resulted in hyperglycemia and spleen somatic index reduction. Glucose elevation and lysozyme activity decreased following repeated hypoxia. Complement hemolytic activity was unchanged regardless of hypoxic stress or domestication level. A 2D-DIGE proteomic analysis showed that some C3 components were positively modulated by single hypoxia while C3 up- and down-regulations and over-expression of transferrin were observed following repeated hypoxia. Domestication was associated with a low divergence in stress and immune responses to hypoxia but was accompanied by various changes in the abundance of serum proteins related to innate/specific immunity and acute phase response. Thus, it appeared that the humoral immune system was modulated following single and repeated hypoxia (independently of generational level) or during domestication and that Eurasian perch may display physiological acclimation to frequent hypoxic disturbances.

Microarray-based identification of differentially expressed genes in families of turbot (Scophthalmus maximus) after infection with viral haemorrhagic septicaemia virus (VHSV)

Viral haemorrhagic septicaemia virus (VHSV) is one of the major threats to the development of the aquaculture industry worldwide. The present study was aimed to identify genes differentially expressed in several turbot (Scophthalmus maximus) families showing different mortality rates after VHSV. The expression analysis was conducted through genome-wide expression profiling with an oligo-microarray in the head kidney. A significant proportion of the variation in the gene expression profiles seemed to be explained by the genetic background, indicating that the mechanisms by which particular species and/or populations can resist a pathogen(s) are complex and multifactorial. Before the experimental infections, fish from resistant families (low mortality rates after VHSV infection) showed high expression of different antimicrobial peptides, suggesting that their pre-immune state may be stronger than fish of susceptible families (high mortality rates after VHSV infection). After infection, fish from both high- and low-mortality families showed an up-modulation of the interferon-induced Mx2 gene, the IL-8 gene and the VHSV-induced protein 5 gene compared with control groups. Low levels of several molecules secreted in the mucus were observed in high-mortality families, but different genes involved in viral entrance into target cells were down-regulated in low-mortality families. Moreover, these families also showed a strong down-modulation of marker genes related to VHSV target organs, including biochemical markers of renal dysfunction and myocardial injury. In general, the expression of different genes involved in the metabolism of sugars, lipids and proteins were decreased in both low- and high-mortality families after infection. The present study serves as an initial screen for genes of interest and provides an extensive overview of the genetic basis underlying the differences between families that are resistant or susceptible to VHSV infection.

[Cloning, physical and chemical property analysis of the Japanese sea bass Wap65-2 gene and its expression following Vibrio harveyi infection]

The warm temperature acclimation related 65 kDa protein-2 (Wap65-2), a teleost plasma glycoprotein, plays an important role in immune regulation against bacterial infection. Here, for the first time we determined the full length cDNA sequence of the Japanese sea bass Wap65-2 gene (1 601 bp in length excluding the 3'-polyA tail). The sequence contains an open reading frame that encodes a protein of 436 amino acids with a molecular weight of 4.87×10(4). The predicted protein had a signal peptide in the N-terminal domain containing 19 residues. Sequence comparison and phylogenetic tree analysis showed that the Japanese sea bass Wap65-2 has a relatively high similarity to the Dicentrarchus labrax Wap65-2. In the healthy Japanese sea bass, Wap65-2 mRNA was expressed mainly in the liver and weakly in the heart and muscle. qRT-PCR results revealed that liver Wap65-2 transcripts were significantly increased after a Vibrio harveyi infection, and peaked 24 hour post injection (6.89 fold increase). The Japanese sea bass Wap65-2 protein was expressed in Escherichia coli and subsequently used for antiserum preparation. Western blot analysis showed that Wap65-2 was significantly increased in V. harveyi infected Japanese sea bass and reached a maximum of 5.33-fold increase at 36 h. In conclusion, the alteration of Japanese sea bass Wap65-2 expression was tightly associated with the progression of the V. harveyi bacterial infection.

Transcriptomic signatures of attachment, NF-κB suppression and IFN stimulation in the catfish gill following columnaris bacterial infection

Outbreaks of columnaris disease (Flavobacterium columnare) are common in wild and cultured freshwater fish worldwide. Disease occurrences, particularly those caused by virulent genomovar II isolates, in aquaculture species such as channel catfish can be devastating. In contrast to other important aquaculture pathogens, little is known about host immune responses to columnaris. Adhesion of F. columnare to gill tissue has been correlated in some previous studies to virulence and host susceptibility. Here, therefore, we conducted the first transcriptomic profiling of host responses to columnaris following an experimental challenge. We utilized Illumina-based RNA-seq expression profiling to examine transcript profiles at three timepoints (4h, 24h, and 48h) in catfish gill after bath immersion infection. Enrichment and pathway analyses of the differentially expressed genes revealed several central signatures following infection. These included the dramatic upregulation of a rhamnose-binding lectin, with putative roles in bacterial attachment and aggregation, suppression of NF-κB signalling via IκBs, BCL-3, TAX1BP1, and olfactomedin 4, and strong induction of IFN-inducible responses including iNOS2b, IFI44, and VHSV genes. Fifteen differentially expressed genes with varying expression profiles by RNA-seq, were validated by QPCR (correlation coefficients 0.85-0.94, p-value <0.001). Our results highlight several putative immune pathways and individual candidate genes deserving of further investigation in the context of development of therapeutic regimens and laying the foundation for selection of resistant catfish lines against columnaris.

New insights into fish swimming: a proteomic and isotopic approach in gilthead sea bream

Moderate exercise enhances fish growth, although underlying physiological mechanisms are not fully known. Here we performed a proteomic and metabolic study in white (WM) and red (RM) muscle of gilthead sea bream juveniles swimming at 1.5 body lengths per second. Continuous swimming for four weeks enhanced fish growth without increasing food intake. Exercise affected muscle energy stores by decreasing lipid and glycogen contents in WM and RM, respectively. Protein synthesis capacity (RNA/protein), energy use (estimated by lipid-δ(13)C and glycogen-δ(13)C), and enzymatic aerobic capacity increased in WM, while protein turnover (expressed by δ(15)N-fractionation) did not change. RM showed no changes in any of these parameters. 2D-PAGE analysis showed that almost 15% of sarcoplasmic protein spots from WM and RM differed in response to exercise, most being over-expressed in WM and under-expressed in RM. Protein identification by MALDI-TOF/TOF-MS and LC-MS/MS revealed exercise-induced enhancement of several pathways in WM (carbohydrate catabolism, protein synthesis, muscle contraction, and detoxification) and under-expression of others in RM (energy production, muscle contraction, and homeostatic processes). The mechanism underpinning the phenotypic response to exercise sheds light on the adaptive processes of fish muscles, being the sustained-moderate swimming induced in gilthead sea bream achieved mainly by WM, thus reducing the work load of RM and improving swimming performance and food conversion efficiency.

Modulation of warm-temperature-acclimation-associated 65-kDa protein genes (Wap65-1 and Wap65-2) in mud loach (Misgurnus mizolepis, Cypriniformes) liver in response to different stimulatory treatments

Two paralogous isoform cDNAs of warm-temperature-acclimation-associated 65-kDa protein (Wap65-1 and Wap65-2) were isolated from the cypriniform species, mud loach (Misgurnus mizolepis), and characterized. The deduced amino acid sequences of the two mud loach Wap65 isoforms (mlWap65-1 and mlWap65-2) share moderate levels of sequence homology with their corresponding orthologues from teleosts and with human hemopexin, a possible mammalian homologue. Both isoforms display conserved features, including essential motifs and/or residues that are important for the protein structure of hemopexin. In overall, mlWap65-2 is more homologous to human hemopexin than is mlWap65-1. Both mud loach Wap65 transcripts are predominantly expressed in liver, although the transcripts are ubiquitously detectable in most tissues with variable basal expression. Both mlWap65 isoforms are differentially regulated during embryonic development, and the changes in transcript levels during embryogenesis are greater for mlWap65-2 than for mlWap65-1. The transcription of the mlWap65 genes is differentially modulated by various stimuli, including thermal changes, immune challenge (lipopolysaccharide injection or bacterial infection), and heavy metal exposure (cadmium, copper, or nickel). The isoform mlWap65-1 is more responsive to warm temperature treatments than mlWap65-2, whereas mlWap65-2 is much more strongly stimulated by immune and heavy metal challenges than is mlWap65-1. Taken together, the results of this study suggest that mud loach Wap65 isoforms are potentially involved in multiple cellular pathways and that the two mud loach Wap65 isoforms undergo functional partitioning or subfunctionalization.

Identification and expression analysis of goose-type lysozyme in half-smooth tongue sole (Cynoglossus semilaevis)

Lysozymes are considered to be potent innate immune molecules against the invasion of bacterial pathogens. The goose-type lysozyme is one of the three major distinct lysozyme types identified in the animal kingdom including teleosts. In this report, we identified, sequenced, and characterized the goose-type lysozyme gene (CsGLys) from half-smooth tongue sole (Cynoglossus semilaevis). The full-length cDNA of CsGLys is 1191 bp in length from the transcription start site to polyadenylation site, including a 91 bp 5'-terminal untranslated region (UTR), a 452 bp 3'-terminal UTR and a 648 bp open reading frame (ORF) of encoding a polypeptide with 215 amino acids. The deduced amino acid sequence of CsGLys possesses a Goose Egg White Lysozyme (GEWL) domain with three conserved residues (E91, D104 and D121) essential for catalytic activity. The CsGLys gene consisting of 2535 bp, was similar to those of other teleost species such as Japanese flounder and large yellow croaker with five exons interrupted by four introns. The 5'-flanking region of CsGLys gene shows several transcriptional factor binding sites related to immune response. Tissue expression profile analysis by quantitative real-time reverse transcription PCR showed that CsGLys mRNA was constitutively expressed in all examined tissues with the predominant expression in skin and the weakest expression in heart. The expression of CsGLys after challenged with bacteria Vibrio anguillarum was up-regulated in blood, head kidney, liver and spleen at 12 h post-infection and it reached the peak level at the same time point with a 19.89-, 4.21-, 14.45- and 10.37-fold increase, respectively, while the CsGLys expression was down-regulated to lower level than the normal level in each tested tissues except in liver from the 48 h until 96 h. These results suggest that CsGLys might play an important role in half-smooth tongue sole host defense against the bacteria infection.

Characterization of common carp transcriptome: sequencing, de novo assembly, annotation and comparative genomics

BACKGROUND

Common carp (Cyprinus carpio) is one of the most important aquaculture species of Cyprinidae with an annual global production of 3.4 million tons, accounting for nearly 14% of the freshwater aquaculture production in the world. Due to the economical and ecological importance of common carp, genomic data are eagerly needed for genetic improvement purpose. However, there is still no sufficient transcriptome data available. The objective of the project is to sequence transcriptome deeply and provide well-assembled transcriptome sequences to common carp research community.

RESULT

Transcriptome sequencing of common carp was performed using Roche 454 platform. A total of 1,418,591 clean ESTs were collected and assembled into 36,811 cDNA contigs, with average length of 888 bp and N50 length of 1,002 bp. Annotation was performed and a total of 19,165 unique proteins were identified from assembled contigs. Gene ontology and KEGG analysis were performed and classified all contigs into functional categories for understanding gene functions and regulation pathways. Open Reading Frames (ORFs) were detected from 29,869 (81.1%) contigs with an average ORF length of 763 bp. From these contigs, 9,625 full-length cDNAs were identified with sequence length from 201 bp to 9,956 bp. Comparative analysis revealed that 27,693(75.2%) contigs have significant similarity to zebrafish Refseq proteins, and 24,371(66.2%), 24,501(66.5%) and 25,025(70.0%) to teraodon, medaka and three-spined stickleback refseq proteins. A total of 2,064 microsatellites were initially identified from 1,730 contigs, and 1,639 unique sequences had sufficient flanking sequences on both sides for primer design.

CONCLUSION

The transcriptome of common carp had been deep sequenced, de novo assembled and characterized, providing the valuable resource for better understanding of common carp genome. The transcriptome data will facilitate future functional studies on common carp genome, and gradually apply in breeding programs of common carp, as well as closely related other Cyprinids.

Effects of waterborne Cu exposure in gilthead sea bream (Sparus aurata): a proteomic approach

Aquatic organisms may suffer from exposure to high Cu concentrations, since this metal is widely used in feed supplementation, in pesticide formulation and as antifouling. Chronic exposure to Cu, even at sub-lethal doses, may strongly affect fish physiology. To date, several biomarkers have been used to detect Cu exposure in fish producing contrasting results. Therefore, we used a proteomic approach to clarify how Cu exposure may affect the serum proteome of gilthead sea bream (Sparus aurata), since serum could be considered a good source of early-biomarkers of Cu toxicosis. For this purpose we exposed juvenile gilthead sea bream to waterborne Cu (0.5 mg/L). Our results indicate that fish tightly regulate circulating Cu levels, which are not affected by metal exposure. This homeostatic control is mainly achieved by the liver, able to excrete high amounts of the metal via bile. Cu exposure caused differential expression of several serum proteins, 10 of which were identified by Mascot and BLAST search. All these proteins, with the exception of growth hormone receptor and γ-glutamyl-carboxylase, can be related to: 1) Cu-induced hepatotoxicity (cytochrome oxidase subunit I, alanine aminotransferase, glutathione S-transferase); 2) potential immunosuppression due to interference of Cu with the inflammation/immunity network (α-1 antitrypsin, angiotensinogen, complement component C3, recombination-activating protein-1 and warm temperature acclimation-related 65 kDa protein).

Use of suppressive subtractive hybridization to identify differentially expressed genes in ayu (Plecoglossus altivelis) associated with Listonella anguillarum infection

Suppressive subtractive hybridization (SSH) was employed to identify differentially expressed genes in ayu (Plecoglossus altivelis) associated with Listonella anguillarum infection. 800 random clones were selected from forward and reverse subtractive libraries and 787 were successfully sequenced. After assembling, 105 contigs and 414 singletons were finally obtained, some of which were immune-related genes. A real-time quantitative PCR (RT-qPCR) analysis of the expression patterns of 28 transcripts showed that the false-positive rate was approximately 7.1%. Furthermore, Wap65-2 was overexpressed in Escherichia coli, purified and used for antiserum preparation. Western blot analysis revealed that serum Wap65-2 of ayu significantly increased after bacterial infection, suggesting that it was a positive acute-phase protein (APP).

The establishment of a library screening method based on yeast two-hybrid system and its use to determine the potential interactions of liver proteins in ayu, Plecoglossus altivelis

Knowledge of specific protein-protein interaction (PPI) is an important component in understanding biological processes and regulatory mechanisms. A library to library screening method (LLS) was established based on yeast two-hybrid (YTH) system in this research, and applied to study the PPIs in ayu liver. In total, 23 out of 55 interaction pairs were found positive through phenotypic identification, with a positive rate of 41.8%. Of the 11 unique PPIs, 9 interactions including FGB/FGG, CaM/Spna2, C9/Apo-AI-1, α₂M/Ft, RPL10/RPL5, C8α/C9, FGG/Apo-AI-1, LECT2/Tf, and Apo-AI-2/C9 were previously reported. The other two PPIs including FGG/CLR and Wap65/C3 are novel, and in vitro co-immunoprecipitation (co-IP) experiments further confirmed these interactions. FGG/CLR interaction might play a role in regulating the inflammatory response. The interaction between Wap65 and C3 hints that Wap65 might function through the complement activation pathways when microbial infection occurs.

Transcriptional responses in juvenile Atlantic cod (Gadus morhua) after exposure to mercury-contaminated sediments obtained near the wreck of the German WW2 submarine U-864, and from Bergen Harbor, Western Norway

The main aim of the present work was to investigate the effects of mercury (Hg)-enriched sediments on fish. Sediments near the sunken German WW2 submarine U-864, which according to historical documents included 67 tons of metallic Hg in its cargo, are enriched of Hg leaking from the wreckage. Juvenile Atlantic cod (Gadus morhua) were exposed to two field-collected polluted sediments (U-864: inorganic Hg and Bergen Harbor (Vågen): inorganic Hg, PCB and PAH) or two comparable reference sediments for 5 weeks in the laboratory, and transcriptional responses evaluated in gills and liver. Gills of fish exposed to the Hg-enriched sunken WW2 submarine U-864 sediment contained four fold higher Hg levels compared to the control fish. An increase in Hg content in liver in the U-864 fish was also observed. The transcriptional results showed that calreticulin, HSP70 and heme oxygenase mRNA were significantly up-regulated in gills in fish exposed to the Hg-enriched sediments, whereas calreticulin, heme oxygenase, transferrin and WAP65 were significantly up-regulated and glutathione peroxidase 4B and zona pellucida 3 were significantly down-regulated in liver tissue. In gills and liver of cod exposed to the mixed-contaminated Vågen sediment, CYP1A showed the highest induction. In conclusion, the experiment shows that sediment-bound Hg is available to the fish and affects the transcription of oxidative stress responsive enzymes, suggesting that the Hg-enriched sediments may negatively affect the local wildlife. Furthermore, the mixed contaminated sediments of Vågen affected similar responses in addition to Ah-receptor mediated responses reflecting exposure to PAHs and PCBs.

Molecular responses of ceruloplasmin to Edwardsiella ictaluri infection and iron overload in channel catfish (Ictalurus punctatus)

Ceruloplasmin is a serum ferroxidase that carries more than 90% of the copper in plasma and has documented roles in iron homeostasis as well as antioxidative functions. In our previous studies, it has been shown that the ceruloplasmin gene is strongly up-regulated in catfish during challenge with Edwardsiella ictaluri. However, little is known about the function of this gene in teleost fish. The objective of this study, therefore, was to characterize the ceruloplasmin gene from channel catfish, determine its genomic organization, profile its patterns of tissue expression, and establish its potential for physiological antioxidant responses in catfish after bacterial infection with E. ictaluri and iron treatment. The genomic organization suggested that the catfish ceruloplasmin gene had 20 exons and 19 introns, encoding 1074 amino acids. Exon sizes of the catfish ceruloplasmin gene were close to or identical with mammalian and zebrafish homologs. Further phylogenetic analyses suggested that the gene was highly conserved through evolution. The catfish ceruloplasmin gene was mapped to both the catfish physical map and linkage map. The catfish ceruloplasmin gene was mainly expressed in liver with limited expression in other tissues, and it was significantly up-regulated in the liver after bacterial infection alone or after co-injection with bacteria and iron-dextran, while expression was not significantly induced with iron-dextran treatment alone.

Emergence of the acute-phase protein hemopexin in jawed vertebrates

When released from damaged erythrocytes free heme not only provides a source of iron for invading bacteria but also highly toxic due to its ability to catalyze free radical formation. Hemopexin (Hx) binds free heme with very high-affinity and thus protects against heme toxicity, sequesters heme from pathogens, and helps conserve valuable iron. Hx is also an acute-phase serum protein (APP), whose expression is induced by inflammation. To date Hx has been identified as far back in phylogeny as bony fish where it is called warm-temperature acclimation-related 65 kDa protein (WAP65), as serum protein levels are increased at elevated environmental temperatures as well as by infection. During analysis of nurse shark (Ginglymostoma cirratum) plasma we isolated a Ni(2+)-binding serum glycoprotein and characterized it as the APP Hx. We subsequently cloned Hx from nurse shark and another cartilaginous fish species, the little skate Leucoraja erinacea. Functional analysis showed shark Hx, like that of mammals, binds heme but is found at unusually high levels in normal shark serum. As an Hx orthologue could not be found in the genomes of jawless vertebrates or lower deuterostomes it appears to have arisen just prior to the emergence of jawed vertebrates, coincident with the second round of genome-wide duplication and the appearance of tetrameric hemoglobin (Hb).

Development of genomic resources in support of sequencing, assembly, and annotation of the catfish genome

Major progress has been made in catfish genomics including construction of high-density genetic linkage maps, BAC-based physical maps, and integration of genetic linkage and physical maps. Large numbers of ESTs have been generated from both channel catfish and blue catfish. Microarray platforms have been developed for the analysis of genome expression. Genome repeat structures are studied, laying grounds for whole genome sequencing. USDA recently approved funding of the whole genome sequencing project of catfish using the next generation sequencing technologies. Generation of the whole genome sequence is a historical landmark of catfish research as it opens the real first step of the long march toward genetic enhancement. The research community needs to be focused on aquaculture performance and production traits, take advantage of the unprecedented genome information and technology, and make real progress toward genetic improvements of aquaculture brood stocks.