Having a BLAST: Searchable transcriptome resources for the gilthead sea bream and the European sea bass

Myomaker and Myomixer Characterization in Gilthead Sea Bream under Different Myogenesis Conditions

Skeletal muscle is formed by multinucleated myofibers originated by waves of hyperplasia and hypertrophy during myogenesis. Tissue damage triggers a regeneration process including new myogenesis and muscular remodeling. During myogenesis, the fusion of myoblasts is a key step that requires different genes' expression, including the fusogens myomaker and myomixer. The present work aimed to characterize these proteins in gilthead sea bream and their possible role in in vitro myogenesis, at different fish ages and during muscle regeneration after induced tissue injury. Myomaker is a transmembrane protein highly conserved among vertebrates, whereas Myomixer is a micropeptide that is moderately conserved. myomaker expression is restricted to skeletal muscle, while the expression of myomixer is more ubiquitous. In primary myocytes culture, myomaker and myomixer expression peaked at day 6 and day 8, respectively. During regeneration, the expression of both fusogens and all the myogenic regulatory factors showed a peak after 16 days post-injury. Moreover, myomaker and myomixer were present at different ages, but in fingerlings there were significantly higher transcript levels than in juveniles or adult fish. Overall, Myomaker and Myomixer are valuable markers of muscle growth that together with other regulatory molecules can provide a deeper understanding of myogenesis regulation in fish.

Specific Evolution and Gene Family Expansion of Complement 3 and Regulatory Factor H in Fish

The complement system comprises a large family of plasma proteins that play a central role in innate and adaptive immunity. To better understand the evolution of the complement system in vertebrates and the contribution of complement to fish immunity comprehensive in silico and expression analysis of the gene repertoire was made. Particular attention was given to C3 and the evolutionary related proteins C4 and C5 and to one of the main regulatory factors of C3b, factor H (Cfh). Phylogenetic and gene linkage analysis confirmed the standing hypothesis that the ancestral c3/c4/c5 gene duplicated early. The duplication of C3 (C3.1 and C3.2) and C4 (C4.1 and C4.2) was likely a consequence of the (1R and 2R) genome tetraploidization events at the origin of the vertebrates. In fish, gene number was not conserved and multiple c3 and cfh sequence related genes were encountered, and phylogenetic analysis of each gene generated two main clusters. Duplication of c3 and cfh genes occurred across the teleosts in a species-specific manner. In common, with other immune gene families the c3 gene expansion in fish emerged through a process of tandem gene duplication. Gilthead sea bream (Sparus aurata), had nine c3 gene transcripts highly expressed in liver although as reported in other fish, extra-hepatic expression also occurs. Differences in the sequence and protein domains of the nine deduced C3 proteins in the gilthead sea bream and the presence of specific cysteine and N-glycosylation residues within each isoform was indicative of functional diversity associated with structure. The diversity of C3 and other complement proteins as well as Cfh in teleosts suggests they may have an enhanced capacity to activate complement through direct interaction of C3 isoforms with pathogenic agents.

Whole brain transcriptomics of intermittently fed individuals of the marine teleost Sparus aurata

A major challenge in fish physiology is to understand the mechanisms underlying the transcriptomic responses of fish brain to food deprivation. Differential gene expression analysis identified in total 2240 transcripts that presented >2-fold change (adjusted p < 0.01) between each treatment and the control group (C). The identity of the transcripts was obtained with annotation against multiple public databases and they were grouped according to their expression patterns. The gene ontology terms that were substantially affected were identified by functional annotation analysis. Genes related to ion transport, cell cycle and cell adhesion were mainly regulated during fasting and refeeding. These findings contribute to identify key indicators for the molecular basis of brain functions during periods of starvation in gilthead seabream.

Molecular and functional regionalization of bicarbonate secretion cascade in the intestine of the European sea bass (Dicentrarchus labrax)

In marine fish the intestinal HCO₃^- secretion is the key mechanism to enable luminal aggregate formation and water absorption. Using the sea bass (Dicentrarchus labrax), the present study aimed at establishing the functional and molecular organization of different sections of the intestine concerning bicarbonate secretion and Cl^- movements. The proximal intestinal regions presented similar HCO₃^- secretion rates, while differences were detected in the molecular expression of the transporters involved and on regional HCO₃^- concentrations. The anterior region presented significantly higher Na⁺/K⁺-ATPase activity, Cl^- transepithelial transport and basolateral slc4a4, apical slc26a6 and slc26a3 expression levels. In the mid intestine, the total HCO₃^- content was significantly increased in the fluid as in the carbonate aggregates. In the rectum no HCO₃^- secretion was observed and was characterized by the diminished HCO₃^- total content, residual molecular expression of slc4a4, slc26a6 and slc26a3, higher H⁺-ATPase activity and expression, suggesting the existence of a different bicarbonate handling mechanism. The possible regulation of HCO₃^- secretion by extracellular HCO₃^- and increased intracellular cAMP levels were also investigated. cAMP did not affect HCO₃^- secretion, although Cl^- secretion was enhanced by cftr. HCO₃^- secretion rise due to the HCO₃^- basolateral increment showed that at resting levels slc4a4 was not a limiting step for secretion. The transcellular/intracellular dependence of apical HCO₃^- secretion differed between the proximal regions. In conclusion, intestinal HCO₃^- secretion has a functional region-dependent organization that was not reflected by the anterior-posterior regionalization on HCO₃^- secretion and expression profiles of chloride/water absorption related genes.

The European sea bass: a key marine fish model in the wild and in aquaculture

The European sea bass (Dicentrarchus labrax L.) is a marine fish of key economic and cultural importance in Europe. It is now more an aquaculture than a fisheries species (>96% of the production in 2016), although modern rearing techniques date back only from the late 1980s. It also has high interest for evolutionary studies, as it is composed of two semispecies (Atlantic and Mediterranean lineages) that have come into secondary contact following the last glaciation. Based on quantitative genetics studies of most traits of interest over the past 10–15 years, selective breeding programs are now applied to this species, which is at the beginning of its domestication process. The availability of a good quality reference genome has accelerated the development of new genomic resources, including SNP arrays that will enable genomic selection to improve genetic gain. There is a need to improve feed efficiency, both for economic and environmental reasons, but this will require novel phenotyping approaches. Further developments will likely focus on the understanding of genotype‐by‐environment interactions, which will be important both for efficient breeding of farmed stocks and for improving knowledge of the evolution of natural populations. At the interface between both, the domestication process must be better understood to improve production and also to fully evaluate the possible impact of aquaculture escapees on wild populations. The latter is an important question for all large‐scale aquaculture productions.

Persistence of the ABCC6 genes and the emergence of the bony skeleton in vertebrates

The ATP-binding cassette transporter 6 (ABCC6) gene encodes a cellular transmembrane protein transporter (MRP6) that is involved in the regulation of tissue calcification in mammals. Mutations in ABCC6 are associated with human ectopic calcification disorders. To gain insight into its evolution and involvement in tissue calcification we conducted a comparative analysis of the ABCC6 gene and the related gene ABCC1 from invertebrates to vertebrates where a bony endoskeleton first evolved. Taking into consideration the role of ABCC6 in ectopic calcification of human skin we analysed the involvement of both genes in the regeneration of scales, mineralized structures that develop in fish skin. The ABCC6 gene was only found in bony vertebrate genomes and was absent from Elasmobranchs, Agnatha and from invertebrates. In teleost fish the abcc6 gene duplicated but the two genes persisted only in some teleost genomes. Six disease causing amino acid mutations in human MRP6 are a normal feature of abcc6 in fish, suggesting they do not have a deleterious effect on the protein. After scale removal the abcc6 (5 and 10 days) and abcc1 (10 days) gene expression was up-regulated relative to the intact control skin and this coincided with a time of intense scale mineralization.

Transcriptome analysis of the brain of the sea bream (Sparus aurata) after exposure to human pharmaceuticals at realistic environmental concentrations

Human pharmaceuticals such as Acetaminophen, Atenolol and Carbamazepine are pseudo persistent aquatic pollutants with yet unknown sub-lethal effects at environmentally relevant concentrations. Gilthead seabream (Sparus aurata) were exposed to Acetaminophen: 31.90 ± 11.07 μg L^-1; Atenolol: 0.95 ± 0.38 μg L^-1 and Carbamazepine: 6.95 ± 0.13 μg L^-1 in a 28 day flow through experiment to (1) determine whether exposure to low concentrations in the μg·L^-1 range of the pharmaceuticals alters the brain transcriptome and, (2) identify different expression profiles and treatment specific modes of action and pathways. Despite low exposure concentrations, 411, 7 and 612 differently expressed transcripts were identified in the individual treatments with Acetaminophen, Atenolol and Carbamazepine, respectively. Functional analyses of differentially expressed genes revealed a significant over representation of several biological processes, cellular compartment features and molecular functions for both Acetaminophen and Carbamazepine treatments. Overall, the results obtained in seabream brain suggest similar physiological responses to those observed in humans also at environmental concentrations, as well as the existence of treatment specific processes that may be useful for the development of biomarkers of contamination.

Thermal imprinting modifies adult stress and innate immune responsiveness in the teleost sea bream

The impact of thermal imprinting on the plasticity of the hypothalamic-pituitary-interrenal (HPI) axis and stress response in an adult ectotherm, the gilthead sea bream (Sparusaurata, L.), during its development was assessed. Fish were reared under 4 thermal regimes, and the resulting adults exposed to acute confinement stress and plasma cortisol levels and genes of the HPI axis were monitored. Changes in immune function, a common result of stress, were also evaluated using histomorphometric measurements of melanomacrophages centers (MMCs) in the head kidney and by monitoring macrophage-related transcripts. Thermal history significantly modified the HPI responsiveness in adult sea bream when eggs and larvae were reared at a higher than optimal temperature (HT, 22°C), and they had a reduced amplitude in their cortisol response and significantly upregulated pituitary pomc and head kidney star transcripts. Additionally, after an acute stress challenge, immune function was modified and the head kidney of adult fish reared during development at high temperatures (HT and LHT, 18-22°C) had a decreased number of MMCs and a significant downregulation of dopachrome tautomerase. Thermal imprinting during development influenced adult sea bream physiology and increased plasma levels of glucose and sodium even in the absence of an acute stress in fish reared under a high-low thermal regime (HLT, 22-18°C). Overall, the results demonstrate that temperature during early development influences the adult HPI axis and immune function in a teleost fish.

Chronic stress impairs the local immune response during cutaneous repair in gilthead sea bream (Sparus aurata, L.)

Scale removal in fish triggers a damage-repair program to re-establish the lost epidermis and scale and an associated local immune response. In mammals, chronic stress is known to delay wound healing and to modulate the cutaneous stress axis, but this is unstudied in teleost fish the most successful extant vertebrates. The present study was designed to test the hypothesis that chronic stress impairs cutaneous repair in teleost fish as a consequence of suppression of the immune response. The hypothesis was tested by removing the scales and damaging the skin on one side of the body of fish previously exposed for 4 weeks to a chronic crowding stress and then evaluating cutaneous repair for 1 week. Scale removal caused the loss of the epidermis although at 3days it was re-established. At this stage the basement membrane was significantly thicker (p=0.038) and the hypodermis was significantly thinner (p=0.016) in the regenerating skin of stressed fish relative to the control fish. At 3days, stressed fish also had a significantly lower plasma osmolality (p=0.015) than control fish indicative of reduced barrier function. Chronic stress caused a significant down-regulation of the glucocorticoid receptor (gr) in skin before damage (time 0, p=0.005) and of star at 3 and 7days (p<0.05) after regeneration relative to control fish. In regenerating skin key transcripts of cutaneous repair, pcna, colivα1 and mmp9, and the inflammatory response, tgfβ1, csf-1r, mpo and crtac2, were down-regulated (p<0.05) by chronic stress. Irrespective of chronic stress and in contrast to intact skin many hyper pigmented masses, putative melanomacrophages, infiltrated the epidermis of regenerating skin. This study reveals that chronic stress suppresses the local immune response to scale removal and impairs the expression of key transcripts of wound healing. Elements of the stress axis were identified and modulated by chronic stress during cutaneous repair in gilthead seabream skin.

Evolution of the angiopoietin-like gene family in teleosts and their role in skin regeneration

BACKGROUND

The skin in vertebrates is a protective barrier and damage is rapidly repaired to re-establish barrier function and maintain internal homeostasis. The angiopoietin-like (ANGPTL) proteins are a family of eight secreted glycoproteins with an important role in skin repair and angiogenesis in humans. In other vertebrates their existence and role in skin remains largely unstudied. The present study characterizes for the first time the homologues of human ANGPTLs in fish and identifies the candidates that share a conserved role in skin repair using a regenerating teleost skin model over a 4-day healing period.

RESULTS

Homologues of human ANGPTL1-7 were identified in fish, although ANGPTL8 was absent and a totally new family member designated angptl9 was identified in fish and other non-mammalian vertebrates. In the teleost fishes a gene family expansion occurred but all the deduced Angptl proteins retained conserved sequence and structure motifs with the human homologues. In sea bream skin angptl1b, angptl2b, angptl4a, angptl4b and angptl7 transcripts were successfully amplified and they were differentially expressed during skin regeneration. In the first 2 days of skin regeneration, re-establishment of the physical barrier and an increase in the number of blood vessels was observed. During the initial stages of skin regeneration angptl1b and angptl2b transcripts were significantly more abundant (p < 0.05) than in intact skin and angptl7 transcripts were down-regulated (p < 0.05) throughout the 4-days of skin regeneration that was studied. No difference in angptl4a and angptl4b transcript abundance was detected during regeneration or between regenerating and intact skin.

CONCLUSIONS

The angptl gene family has expanded in teleost genomes. In sea bream, changes in the expression of angptl1b, angptl2b and angptl7 were correlated with the main phases of skin regeneration, indicating the involvement of ANGPTL family members in skin regeneration has been conserved in the vertebrates. Exploration of the fish angptl family in skin sheds new light on the understanding of the molecular basis of skin regeneration an issue of importance for disease control in aquaculture.