Differential gene expression and dependence on thyroid hormones of two glyceraldehyde-3-phosphate dehydrogenases in the flatfish Senegalese sole (Solea senegalensis Kaup)

The Use of Sand Substrate Modulates Dominance Behaviour and Brain Gene Expression in a Flatfish Species

Physical complexity adds physical enrichment to rearing conditions. This enrichment promotes fish welfare and reduces detrimental characteristics that fish develop in captivity. Senegalese sole (Solea senegalensis) is an important species for European aquaculture, where it is reared in intensive conditions using fibreglass tanks. However, reproductive dysfunctions present in this species do not allow it to complete its life cycle in captivity. Recently, dominance behaviour has been studied to try to solve this problem. The present study aimed to assess the effect of sand as environmental enrichment in the dominance behaviour and brain mRNA abundance of Senegalese sole juveniles. Four tanks of sole (n = 48 fish in total) were established in two different environments (with and without sand). Juveniles were subjected to dominance tests of feeding and territoriality. Behaviours analysed by video recordings related to the distance from the food delivered and harassment behaviour towards other individuals (e.g., resting of the head on another individual). In both environments, dominant sole were the first to feed, displayed more head-resting behaviour and dominated the area close to the feeding point, where the events were reduced in fish maintained in the sand. mRNA expression related to differentiation of dopamine neurons (nr4a2) and regulation of maturation (fshra) were significantly upregulated in dominant fish in the sand environment compared to dominants maintained without sand. The use of an enriched environment may affect Senegalese sole dominance, enhance welfare and possibly advance future maturation.

Proteomic Analysis of the Intestinal Resistance to Thyroid Hormone Mouse Model With Thyroid Hormone Receptor Alpha Mutations

Thyroid hormone is critical during the development of vertebrates and affects the function of many organs and tissues, especially the intestine. Triiodothyronine (T₃) is the active form and can bind to thyroid hormone nuclear receptors (TRs) to play a vital role in the development of vertebrates. The resistance to thyroid hormone α, as seen in patients, has been mimicked by the Thra^E403X mutation. To investigate the mechanisms underlying the effect of TRα1 on intestinal development, the present study employed proteomic analysis to identify differentially expressed proteins (DEPs) in the distal ileum between homozygous Thra^E403X/E403X and wild-type Thra^+/+ mice. A total of 1,189 DEPs were identified, including 603 upregulated and 586 downregulated proteins. Proteomic analysis revealed that the DEPs were highly enriched in the metabolic process, the developmental process, the transporter of the nutrients, and the intestinal immune system-related pathway. Of these DEPs, 20 proteins were validated by parallel reaction monitoring analysis. Our intestinal proteomic results provide promising candidates for future studies, as they suggest novel mechanisms by which TRα1 may influence intestinal development, such as the transport of intestinal nutrients and the establishment of innate and adaptive immune barriers of the intestine.

Linking stress coping styles with brain mRNA abundance of selected transcripts for Senegalese sole (Solea senegalensis) juveniles

In fish, proactive and reactive individual stress copying styles (SCS) have been used to resolve variation in molecular expression data. Stress coping styles have been previously described in several stages of Solea senegalensis by validating for the species the use of standard behavioural screening tests. The present study aimed to link behavioural SCS tests with brain transcript abundance in early Senegalese sole juveniles in order to observe the natural variation in a molecular pathway in this species. A total of 50 juveniles were subjected to three individual behavioural (Restraining, New environment and Confinement) and one group (Risk-taking) screening tests. The fish were classified in SCS categories by applying a hierarchical cluster to the variable "Total activity" (the total activity time that the fish was moving in each individual test). Three categories were defined, proactive, intermediate and reactive sole. Six transcripts were chosen and tested, one related to basic metabolism (gapdh-2), three to feeding behaviour (per1, igf-Ia, pparß) and two to the stress response (crh-BP and hsp90aa) in 30 juveniles (10 individuals per SCS category) using rt-qPCR to observe differences in the abundance of those transcripts among SCS. Four transcripts were differentially expressed (DETs) among them. The transcript gapdh-2 showed up-regulation for proactive and intermediate SCS sole while reactive individuals showed down-regulation. Target mRNAs per1, igf-Ia and pparß, showed different levels of up-regulation for proactive and reactive fish while intermediates were highly down-regulated. Surprisingly no differences in stress related transcripts were observed. Correlations were found between variation in coping styles and variation in the abundance of mRNAs involved in important biological functions in Senegalese sole. These results are the first evidence of the relationship between the behavioural individual variation and the fluctuation in brain transcripts abundance in Senegalese sole.

Coordinated expression and regulation of deiodinases and thyroid hormone receptors during metamorphosis in the Japanese flounder (Paralichthys olivaceus)

In vertebrates, thyroid hormone receptors (TRs) and deiodinases are essential for developmental events driven by the thyroid hormones (THs). However, the significance of deiodinases during the metamorphosis of the Japanese flounder (Paralichthys olivaceus) remains unclear. Moreover, regulation and response of the TRs and deiodinases to THs in this fish are poorly understood. Therefore, we detected the expression patterns of THs, deiodinases, and TRs in drug-treated larvae and untreated larvae of P. olivaceus by using enzyme-linked immunosorbent assay and quantitative real-time PCR during P. olivaceus metamorphosis. To further understand the roles of these elements, a rescue assay was performed. Our results show the importance of THs, TRs, and deiodinases in flatfish metamorphosis. Our results also confirm that D1 and D2 activate THs and D3 plays the opposite and complementary role. Moreover, we demonstrated that both TRα and TRβ have important but different roles during P. olivaceus metamorphosis.

Transcriptomic profiles of the upper olfactory rosette in cultured and wild Senegalese sole (Solea senegalensis) males

The aims of this study were the characterization of the upper olfactory epithelium of cultured and wild Senegalese sole mature males at histological and transcriptomic (using RNA-Seq) level. No significant differences in tissue structure, cell types and cellular distribution pattern (olfactory sensory neurons) were identified between cultured and wild specimens. Deep transcriptomic analysis showed 2387 transcripts were differentially expressed between cultured and wild groups. A detailed analysis identified the differentially expressed transcripts included some olfactory receptors (OR, TAAR and V2R-like) and transcripts related with the control of reproduction such as the brain aromatase cytochrome P450 and tachykinin-3. Also a wide set of genes related with lipid sensing, metabolism and transport were differentially expressed and these transcripts were often down-regulated in cultured fish. Furthermore, cultured males presented a higher expression of genes related with goblet cells and mucin production that modulates innate and adaptive immune responses. All these changes in gene expression could be explained by different nutritional status and diet preference. The different expression of transcripts related to olfaction, reproduction, nutrient sensing and immune system demonstrate distinct differences in functionalities between cultured and wild soles providing new clues about the sexual dysfunction in this species.

Molecular characterization and developmental expression patterns of apolipoprotein A-I in Senegalese sole (Solea senegalensis Kaup)

The apolipoprotein A-I (ApoA-I) is an essential component of the high density lipoproteins (HDL). In this study, the cDNA and genomic sequences of this apolipoprotein were characterized for first time in Solea senegalensis. The predicted polypeptide revealed conserved structural features including ten repeats in the lipid-binding domain and some residues involved in cholesterol interaction and binding. The gene structure analysis identified four exons and three introns. Moreover, the synteny analysis revealed that apoA-I did not localize with other apolipoproteins indicating a divergent evolution with respect to the apoA-IV and apoE cluster. The phylogenetic analyses identified two distinct apoA-I paralogs in Ostariophysi (referred to as Ia and Ib) and only one (Ib) in Acanthopterygii. Whole-mount in situ hybridization located the apoA-I signal mainly in the yolk syncytial layer in lecitotrophic larval stages. Later at mouth opening, the mRNA signals were detected mainly in liver and intestine compatible with its role in the HDL formation. Moreover, a clear signal was detected in some regions of the brain, retina and neural cord suggesting a role in local regulation of cholesterol homeostasis. After metamorphosis, apoA-I was also detected in other tissues such as gills, head kidney and spleen suggesting a putative role in immunity. Expression analyses in larvae fed two diets with different triacylglycerol levels indicated that apoA-I mRNA levels were more associated to larval size and development than dietary lipid levels. Finally, qPCR analyses of immature and mature transcripts revealed distinct expression profiles suggesting a posttranscriptional regulatory mechanism.

Genomic characterization and expression analysis of four apolipoprotein A-IV paralogs in Senegalese sole (Solea senegalensis Kaup)

The apolipoprotein A-IV (ApoA-IV) plays a key role in lipid transport and feed intake regulation. In this work, four cDNA sequences encoding ApoA-IV paralogs were identified. Sequence analysis revealed conserved structural features including the common 33-codon block and nine repeated motifs. Gene structure analysis identified four exons and three introns except for apoA-IVAa1 (with only 3 exons). Synteny analysis showed that the four paralogs were structured into two clusters (cluster A containing apoA-IVAa1 and apoA-IVAa2 and cluster B with apoA-IVBa3 and apoA-IVBa4) linked to an apolipoprotein E. Phylogenetic analysis clearly separated the paralogs according to their cluster organization as well as revealed four subclades highly conserved in Acanthopterygii. Whole-mount analyses (WISH) in early larvae (0 and 1day post-hatch (dph)) showed that the four paralogs were mainly expressed in yolk syncytial layer surrounding the oil globules. Later, at 3 and 5dph, the four paralogs were mainly expressed in liver and intestine although with differences in their relative abundance and temporal expression patterns. Diet supply triggered the intensity of WISH signals in the intestine of the four paralogs. Quantification of mRNA abundance by qPCR using whole larvae only detected the induction by diet at 5dph. Moreover, transcript levels increased progressively with age except for apoA-IVAa2, which appeared as a low-expressed isoform. Expression analysis in juvenile tissues confirmed that the four paralogs were mainly expressed in liver and intestine and secondary in other tissues. The role of these ApoA-IV genes in lipid transport and the possible role of apoA-IVAa2 as a regulatory form are discussed.

Flatfish metamorphosis: a hypothalamic independent process?

Anuran and flatfish metamorphosis are tightly regulated by thyroid hormones that are the necessary and sufficient factors that drive this developmental event. In the present study whole mount in situ hybridization (WISH) and quantitative PCR in sole are used to explore the central regulation of flatfish metamorphosis. Central regulation of the thyroid in vertebrates is mediated by the hypothalamus-pituitary-thyroid (HPT) axis. Teleosts diverge from other vertebrates as hypothalamic regulation in the HPT axis is proposed to be through hypothalamic inhibition although the regulatory factor remains enigmatic. The dynamics of the HPT axis during sole metamorphosis revealed integration between the activity of the thyrotrophes in the pituitary and the thyroid follicles. No evidence was found supporting a role for thyroid releasing hormone (trh) or corticotrophin releasing hormone (crh) in hypothalamic control of TH production during sole metamorphosis. Intriguingly the results of the present study suggest that neither hypothalamic trh nor crh expression changes during sole metamorphosis and raises questions about the role of these factors and the hypothalamus in regulation of thyrotrophs.

De novo assembly, characterization and functional annotation of Senegalese sole (Solea senegalensis) and common sole (Solea solea) transcriptomes: integration in a database and design of a microarray

Background

Senegalese sole (Solea senegalensis) and common sole (S. solea) are two economically and evolutionary important flatfish species both in fisheries and aquaculture. Although some genomic resources and tools were recently described in these species, further sequencing efforts are required to establish a complete transcriptome, and to identify new molecular markers. Moreover, the comparative analysis of transcriptomes will be useful to understand flatfish evolution.

Results

A comprehensive characterization of the transcriptome for each species was carried out using a large set of Illumina data (more than 1,800 millions reads for each sole species) and 454 reads (more than 5 millions reads only in S. senegalensis), providing coverages ranging from 1,384x to 2,543x. After a de novo assembly, 45,063 and 38,402 different transcripts were obtained, comprising 18,738 and 22,683 full-length cDNAs in S. senegalensis and S. solea, respectively. A reference transcriptome with the longest unique transcripts and putative non-redundant new transcripts was established for each species. A subset of 11,953 reference transcripts was qualified as highly reliable orthologs (>97% identity) between both species. A small subset of putative species-specific, lineage-specific and flatfish-specific transcripts were also identified. Furthermore, transcriptome data permitted the identification of single nucleotide polymorphisms and simple-sequence repeats confirmed by FISH to be used in further genetic and expression studies. Moreover, evidences on the retention of crystallins crybb1, crybb1-like and crybb3 in the two species of soles are also presented. Transcriptome information was applied to the design of a microarray tool in S. senegalensis that was successfully tested and validated by qPCR. Finally, transcriptomic data were hosted and structured at SoleaDB.

Conclusions

Transcriptomes and molecular markers identified in this study represent a valuable source for future genomic studies in these economically important species. Orthology analysis provided new clues regarding sole genome evolution indicating a divergent evolution of crystallins in flatfish. The design of a microarray and establishment of a reference transcriptome will be useful for large-scale gene expression studies. Moreover, the integration of transcriptomic data in the SoleaDB will facilitate the management of genomic information in these important species.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-952) contains supplementary material, which is available to authorized users.

Molecular characterization and transcriptional regulation of the Na +/K+ ATPase α subunit isoforms during development and salinity challenge in a teleost fish, the Senegalese sole (Solea senegalensis)

In the present work, five genes encoding different Na(+),K(+) ATPase (NKA) α-isoforms in the teleost Solea senegalensis are described for the first time. Sequence analysis of predicted polypeptides revealed a high degree of conservation across teleosts and mammals. Phylogenetic analysis clustered the five genes into three main clades: α1 (designated atp1a1a and atp1a1b), α2 (designated atp1a2) and α3 (designated atp1a3a and atp1a3b) isoforms. Transcriptional analysis in larvae showed distinct expression profiles during development. In juvenile tissues, the atp1a1a gene was highly expressed in osmoregulatory organs, atp1a2 in skeletal muscle, atp1a1b in brain and heart and atp1a3a and atp1a3b mainly in brain. Quantification of mRNA abundance after a salinity challenge showed that atp1a1a transcript levels increased significantly in the gill of soles transferred to high salinity water (60 ppt). In contrast, atp1a3a transcripts increased at low salinity (5 ppt). In situ hybridization (ISH) analysis revealed that the number of ionocytes expressing atp1a1a transcripts in the primary gill filaments was higher at 35 and 60 ppt than at 5 ppt and remained undetectable or at very low levels in the lamellae at 5 and 35 ppt but increased at 60 ppt. Immunohistochemistry showed a higher number of positive cells in the lamellae. Whole-mount analysis of atp1a1a mRNA in young sole larvae revealed that it was localized in gut, pronephric tubule, gill, otic vesicle, yolk sac ionocytes and chordacentrum. Moreover, atp1a1a mRNAs increased at mouth opening (3 DPH) in larvae incubated at 36 ppt with a greater signal in gills.

EF1α is a useful internal reference for studies of gene expression regulation in amphioxus Branchiostoma japonicum

Amphioxus is a well-known model organism widely used for interspecies comparative genome study, developmental homology analysis and comparative immunological investigation. However, no study has been performed so far to evaluate the internal reference for quantitative RT-PCR (qRT-PCR) studies of gene expression in this important species. In this study, two software applications (geNorm and NormFinder) were used to evaluate the expression stability of 4 housekeeping genes (ACTB, GAPDH, 18S rRNA and EF1α) in 8 different normal tissues (whole body, gut, gut-free body, hepatic caecum, gill, hind-gut, notochord and muscle) and 2 tissues (gut and gut-free body) challenged with LPS and LTA in amphioxus Branchiostoma japonicum. Our results showed that in the normal tissues, the expression of 18S rRNA was most abundant, whereas the expression levels of the other three genes were close to each other, with the expression of ACTB being most unstable. Following challenge with LPS and LTA, all the four genes exhibited varied degrees of expression changes in the different tissues and the expression stabilities of the genes were also affected by the different experimental conditions. Yet, the overall ranking results produced by the two algorithms consistently indicated that the expression of EF1α showed the most least variation in the different tissues, suggesting that EF1α is a suitable internal control for qRT-PCR studies in amphioxus B. japonicum.

Dexamethasone modulates expression of genes involved in the innate immune system, growth and stress and increases susceptibility to bacterial disease in Senegalese sole (Solea senegalensis Kaup, 1858)

Cortisol, the main glucocorticoid in fish, undertakes pleiotropic biological effects in response to stressors to maintain homeostasis. It can exert several actions on the immune system, growth and cellular metabolism, establishing a fine-tune regulation stress response and cross-talk interactions with other regulatory pathways. In this study, we investigated a causal relationship between high levels of glucocorticoids and susceptibility to pathogens and modification of gene expression profiles in Senegalese sole. For this purpose, we carried out two experiments using post-metamorphic individuals (21 days after hatching) that were exposed to dexamethasone (DXM), a potent glucocorticoid, in order to mimic cortisol effects. We quantified transcript levels of a wide set of genes involved in innate immune system (g-type lysozyme and hepcidin (hamp1)), HPI axis (crf, crfbp, pomcα, pomcβ, gr1 and gr2), HPT axis (tgb), cellular stress defense system (hsp70 and hsp90aa), GH/IGF axis (igf-I and igf-Ir) and the neuropeptide trh. Short-term exposure to 0.1, 1 and 10 ppm DXM provoked a reduction of pomcβ transcripts and an increase of crfbp mRNAs in a dose-dependent manner at 48 and 72 h after treatment. Moreover, g-type lysozyme transcript levels decreased significantly at 72 h whereas hamp1 mRNA levels increased at 48 h after exposure. Long-term DXM treatment (10 ppm DXM) affected negatively weight of soles (~20% lower than controls). Moreover, reduced mRNA levels were observed for pomcβ after 1 week and igf-I and hamp1 after 2 weeks. In contrast, crfbp and crf increased mRNA levels after 2 weeks. hsp70 exhibited a dual response increasing transcript levels at 1 week after treatment and reducing thereafter. No significant changes in gene expression were observed at any time during this study for tgb, trh, hsp90aa, pomcα, gr1 and gr2. Finally, a challenge experiment using the pathogen Photobacterium damselae subsp piscicida confirmed earlier and higher mortalities in DXM-treated animals. Taken together, these data indicate that a prolonged exposure to DXM increases the susceptibility to pathogens and reduces growth. Moreover, DXM can trigger a wide cellular response modulating the expression of genes involved in the innate immune system, HPI and GH/IGF axes as well as cellular stress defense. These results are highly valuable to evaluate responses associated to aquaculture stressful conditions and discriminate specific glucocorticoid-mediated effects.

Functional divergences of GAPDH isoforms during early development in two perciform fish species

Glyceraldehyde-3-phospate dehydrogenase (GAPDH) is involved in basic cell catabolic processes and, as it is thought to be continuously expressed, belongs to the group of housekeeping genes. Thus, it is frequently used as an internal control in quantitative gene expression studies. However, the evidence of different expression patterns in a broad range of organisms and tissues, as well as the occurrence of different isoforms, shows that GAPDH has to be reevaluated as an internal control in qPCR studies, and its annotation has to be enriched. GAPDH has been shown to be involved in the pathway of energy and carbon molecule supply as well as in transcription and apoptosis. In the present study, we isolated the two isoforms, GAPDH-1 and GAPDH-2, of the gilthead sea bream (Sparus aurata) and the European sea bass (Dicentrarchus labrax). We inferred the phylogenetic relationships to ten other fish species and gave the gene structure of both genes. We further investigated gene expression analysis in both species for different developmental stages showing divergent gene expression of the two isoforms and the possible function of GAPDH-1 as a maternal gene.

Genomic characterization, phylogeny and gene regulation of g-type lysozyme in sole (Solea senegalensis)

The g-type lysozyme is a key protein of the innate immune system to fight bacterial infections. In this study we cloned and characterized the gene encoding for g-type lysozyme in Senegalese sole (Solea senegalensis). The deduced amino acid sequence comprised 195 residues containing the three conserved catalytic residues and two cysteines. A BAC analysis revealed that the gene is structured in 5 exons and 4 introns. Also, two polyadenylation signals that generate two cDNAs differing in 3'-UTR length were detected. Promoter analysis showed the presence of the main cis-acting elements involved in the transcriptional regulation of the gene. At genomic level, the g-type lysozyme was associated with mucolipin 1 and the peptidoglycan recognition protein 2 conforming a cluster of antidefensive genes with a well-conserved synteny across Percomorpha. FISH analysis using the BAC clone revealed a single hybridization signal located in an acrocentric chromosome pair. The phylogenetic analysis confirmed that the g-type lysozyme represents a complex group in fish that has been shaped by gene duplications and diversification with several positions under Darwinian selection. Expression analysis in juvenile tissues indicated that transcript levels were higher in gills, spleen and heart. During development, gene expression activated just at the beginning of metamorphosis, increasing progressively until climax. Hormonal treatments demonstrated that this gene was regulated positively by thyroid hormones during development and negatively by dexamethasone. In contrast, no response was observed after all-trans retinoic acid or 4-diethylaminobenzaldehyde treatments. Finally, treatments using lipopolysaccharide, lipoteichoic acid, peptidoglycan, zymosan and poly(I:C) activated gene expression in a time- and tissue-specific manner. Taken together, data indicate that g-type lysozyme is a high evolutionary conserved gene that diversified to adapt to changing environment and pathogen conditions. Gene expression can be activated by diverse pathogen stimuli and modulated by physiological factors with important consequences for the aquaculture of this species.

Molecular characterization and transcriptional regulation of the sodium-dependent vitamin C transporter genes (slc23a1 and slc23a2) in a teleost fish, the Senegalese sole (Solea senegalensis)

Vitamin C (ascorbic acid, AA) is an antioxidant that acts as a free radical scavenger and cofactor for several important enzymatic reactions, thus being important for normal cellular functions, growth and development. Accumulation of AA in cells depends on two types of sodium-dependent vitamin C transporters (SVCTs), designed as SVCT1 and SVCT2. In human, they are the products of SLC23A1 and SLC23A2 genes, respectively. In the present work, the molecular cloning of the cDNAs corresponding to slc23a1 and slc23a2 in a teleost fish, the Senegalese sole (Solea senegalensis Kaup, 1858) is first described. Sequence analysis of the predicted polypeptides revealed a conserved topology with those of mammals with important motifs involved in structure and function, being also present in svct1 and svct2. Phylogenetic analyses including a range of vertebrate SVCTs suggest that both transporters are the result of an ancient gene duplication event that occurred prior to the divergence of tetrapods and teleosts, which took place 450 million years ago. Expression profiles in juvenile tissues and during larval development were analyzed using a real-time PCR approach. In juvenile fish, slc23a1 was strongly expressed in intestine, whereas slc23a2 exhibited a widespread distribution in tissues. Transcripts of both genes were detected at early developmental stages, probably representing mRNAs of maternal origin. A possible regulation by their own substrate was detected after first uptakes of AA from diet in both genes. During metamorphosis, both slc23a1 and slc23a2 were down-regulated, the former in a thyroid hormone (TH) dependent way. This pattern coincided with a significant reduction in the AA content of larvae during metamorphosis. These results are interpreted in a physiological context of general reduction in the metabolism of metamorphic larvae. Data presented here provide the first step toward a better understanding of the physiological role of SVCTs in teleost fish.

Testis-specific glyceraldehyde-3-phosphate dehydrogenase: origin and evolution

Background

Glyceraldehyde-3-phosphate dehydrogenase (GAPD) catalyses one of the glycolytic reactions and is also involved in a number of non-glycolytic processes, such as endocytosis, DNA excision repair, and induction of apoptosis. Mammals are known to possess two homologous GAPD isoenzymes: GAPD-1, a well-studied protein found in all somatic cells, and GAPD-2, which is expressed solely in testis. GAPD-2 supplies energy required for the movement of spermatozoa and is tightly bound to the sperm tail cytoskeleton by the additional N-terminal proline-rich domain absent in GAPD-1. In this study we investigate the evolutionary history of GAPD and gain some insights into specialization of GAPD-2 as a testis-specific protein.

Results

A dataset of GAPD sequences was assembled from public databases and used for phylogeny reconstruction by means of the Bayesian method. Since resolution in some clades of the obtained tree was too low, syntenic analysis was carried out to define the evolutionary history of GAPD more precisely. The performed selection tests showed that selective pressure varies across lineages and isoenzymes, as well as across different regions of the same sequences.

Conclusions

The obtained results suggest that GAPD-1 and GAPD-2 emerged after duplication during the early evolution of chordates. GAPD-2 was subsequently lost by most lineages except lizards, mammals, as well as cartilaginous and bony fishes. In reptilians and mammals, GAPD-2 specialized to a testis-specific protein and acquired the novel N-terminal proline-rich domain anchoring the protein in the sperm tail cytoskeleton. This domain is likely to have originated by exonization of a microsatellite genomic region. Recognition of the proline-rich domain by cytoskeletal proteins seems to be unspecific. Besides testis, GAPD-2 of lizards was also found in some regenerating tissues, but it lacks the proline-rich domain due to tissue-specific alternative splicing.

Effect of different diets on proteolytic enzyme activity, trypsinogen gene expression and dietary carbon assimilation in Senegalese sole (Solea senegalensis) larvae

The effect of diet on larval growth, anionic trypsinogen gene expression (ssetryp1), and trypsin (EC 3.4.21.4) and chymotrypsin (EC 3.4.21.1) activities was assessed in Solea senegalensis. Changes in larval carbon stable isotope (δ(13)C) composition were used to estimate carbon assimilation. Diets were supplied for 20days to fish held in larval rearing tanks and consisted of live rotifers, Artemia sp. nauplii, rotifers followed by Artemia sp., rotifers co-fed with inert diet and inert diet alone. Growth was significantly faster in larvae fed only Artemia and those fed rotifers and Artemia (k=0.381-0.387day(-1)). Trypsin and chymotrypsin activities increased from 3 to 4days after hatching (DAH) in all dietary treatments, while ssetryp1 transcripts increased at 4-5 DAH only in larvae fed live prey. ssetryp1 gene expression was activated later in larvae fed only Artemia and this corresponded with Artemia δ(13)C values being reflected in larval tissue. Larval δ(13)C values also indicated greater selection and/or assimilation of rotifers in relation to the inert diet. Results demonstrate that during early larval development of sole, diet modulates ssetryp1 gene expression. The rapid and intense response to diets that promoted different growth and survival suggests the suitability of this biomarker as a nutritional status indicator in early sole larvae.

Molecular characterization and gene expression of thyrotropin receptor (TSHR) and a truncated TSHR-like in Senegalese sole

Thyroid hormones (THs) play a key role in larval development, growth and metamorphosis in flatfish. Their synthesis is tightly regulated by the hypothalamic-pituitary-thyroid axis. Thyroid-stimulating hormone receptor (TSHR) is a key protein in the control of thyroid function stimulating TH synthesis after binding its ligand, the thyrotropin. In teleost fish, numerous reports have associated the TSHR with gametogenesis. However, little information about its role during larval development is available. In this study, we report the cloning of two different cDNAs with high similarity to TSHR. Phylogenetic analysis clustered both cDNAs separately. One of them (referred to TSHR) grouped with TSHR orthologs in tetrapods and teleost fish and possessed the three typical conserved domains and regulatory motifs. The second receptor (referred to as TSHRtr-like) represented a novel truncated cDNA bearing the extracellular and part of the transmembrane domain. TSHRtr-like orthologs were only found in teleosts, which suggests that it could have appeared after fish-specific 3R genome duplication. Expression profiles of both genes are analyzed in juvenile tissues and during larval development using a real-time PCR approach. In juvenile fish, TSHR and TSHRtr-like are expressed ubiquitously although transcript levels varied between organs. In both cases, the highest mRNAs levels are detected in brain. During larval development, both genes are expressed to a high level during the first stages (2-3days after hatching) reducing progressively their abundance in the whole larvae during metamorphosis. This reduction in mRNA abundance is more accentuated for the TSHRtr-like gene. To evaluate the possible regulation of both receptors by T4 during sole metamorphosis, larvae are exposed to the goitrogen thiourea (TU). Only TSHRtr-like modifies its expression, increasing its transcripts at 11days after treatment. Moreover, adding exogenous T4 hormone to TU-treated larvae restores the TSHRtr-like steady-state levels similar to the untreated control. Overall, these results demonstrate the existence of two thyrotropin receptors differentially regulated by THs in teleosts.

Solea senegalensis genes responding to lipopolysaccharide and copper sulphate challenges: large-scale identification by suppression subtractive hybridization and absolute quantification of transcriptional profiles by real-time RT-PCR

Solea senegalensis is a commercially relevant aquaculture species that remains largely unexplored at the genomic level. The aim of this study was to identify novel genomic responses to lipopolysaccharide and copper sulphate challenges using suppression subtractive hybridization (SSH) and real-time RT-PCR. Forward- and reverse-subtractive libraries were generated for the identification of genes whose transcription is altered in response to lipopolysaccharide (LPS) (immunomodulator) in head kidney (immunologically important organ) and to CuSO(4) (common algacide) in liver (central metabolic organ and important source of immune transcripts). A total of 156 genes involved in major physiological functions were identified by SSH, the identified sequences representing a significant increase in the number of sole ESTs in public databases. Fifteen genes represented in the subtracted libraries were selected for further tissue, temporal and inducible transcriptional profiling by real-time RT-PCR. A rigorous quantification of transcript copy numbers was performed for this purpose in both pooled and individual samples from two independent experiments. More than half of the investigated mRNAs encode proteins that deal with different aspects of the immune response, like NCCRP1 (non-specific cytotoxic cell receptor), C3 and C7 (complement components), and ferritin M, HP and TF (iron homeostasis), or play a crucial role in its regulation, like TRAF3. Other mRNAs studied encode proteins involved in metabolism, like TKT and NDUFA4, the response to stimulus, like CEBPB (transcription factor) and CIRBP (RNA-binding protein), and other cell processes. Highly abundant (>500 molecules/pg total RNA) and rare (< or =1 molecules/pg) mRNA species were quantified in each sole organ examined, and outstanding differences were also recorded in the comparison between the two organs, e.g. C3 and TF mRNAs were largely overexpressed in liver (>5000 molecules/pg) as compared to head kidney (<5 molecules/pg). Most investigated mRNAs displayed significant alterations in their steady-state copy number following LPS and/or CuSO(4) stimulation, i.e. they were (i) up-regulated in response to both treatments in at least one of the two organs (NCCRP1, CEBPB, SQSTM1, NDUFA4, C7 and HP), (ii) up-regulated (TF, CIRBP, TRFA, C3) or down-regulated (TKT) by LPS, their levels remaining essentially unchanged upon CuSO(4) challenge, or (iii) down-regulated by LPS, though up-regulated by CuSO(4) (ferritin M). Quantifications in individual fish were consistent with those in pooled samples with respect to both the direction and the absolute changes in transcript abundance.

Molecular characterization, gene expression and transcriptional regulation of thyroid hormone receptors in Senegalese sole

Thyroid hormones (THs) play a key role in larval development, growth and metamorphosis in flatfish. Their genomic effects are mediated by thyroid hormone receptors (TRs). In this study, cDNAs encoding for TRalphaA, TRalphaB, and TRbeta have been sequenced in Senegalese sole (Soleasenegalensis). Main domains and conserved motifs were identified. Also, a truncated TRalphaB isoform (referred to as TRalphaBtr) and a spliced TRbeta variant (referred to as TRbetav) were detected. A phylogenetic analysis grouped both TRalpha and TRbeta genes into two separate clusters with their fish and mammalian counterparts. Expression profiles during larval development and in juvenile tissues were analyzed using a real-time PCR approach. In juvenile fish, TRalphaA, TRalphaB, TRbetav, and TRbeta showed distinct transcript levels in tissues. During metamorphosis, only TRbetav and TRbeta modified their mRNA levels in a similar way to the T4 contents. To evaluate the possible regulation of TRs by their cognate ligand T4 during sole metamorphosis, larvae were exposed to the goitrogen thiourea (TU). TRbeta transcripts decreased significantly at 11 and 15 days after treatment. Moreover, adding exogenous T4 hormone to TU-treated larvae restored the steady-state levels or even increased TRbeta and TRbetav mRNAs with respect to the untreated control. Overall, these results demonstrate that TRbeta transcription is up-regulated by THs playing a major role during metamorphosis in Senegalese sole.

Genomic resources for a commercial flatfish, the Senegalese sole (Solea senegalensis): EST sequencing, oligo microarray design, and development of the Soleamold bioinformatic platform

Background

The Senegalese sole, Solea senegalensis, is a highly prized flatfish of growing commercial interest for aquaculture in Southern Europe. However, despite the industrial production of Senegalese sole being hampered primarily by lack of information on the physiological mechanisms involved in reproduction, growth and immunity, very limited genomic information is available on this species.

Results

Sequencing of a S. senegalensis multi-tissue normalized cDNA library, from adult tissues (brain, stomach, intestine, liver, ovary, and testis), larval stages (pre-metamorphosis, metamorphosis), juvenile stages (post-metamorphosis, abnormal fish), and undifferentiated gonads, generated 10,185 expressed sequence tags (ESTs). Clones were sequenced from the 3'-end to identify isoform specific sequences. Assembly of the entire EST collection into contigs gave 5,208 unique sequences of which 1,769 (34%) had matches in GenBank, thus showing a low level of redundancy. The sequence of the 5,208 unigenes was used to design and validate an oligonucleotide microarray representing 5,087 unique Senegalese sole transcripts. Finally, a novel interactive bioinformatic platform, Soleamold, was developed for the Senegalese sole EST collection as well as microarray and ISH data.

Conclusion

New genomic resources have been developed for S. senegalensis, an economically important fish in aquaculture, which include a collection of expressed genes, an oligonucleotide microarray, and a publicly available bioinformatic platform that can be used to study gene expression in this species. These resources will help elucidate transcriptional regulation in wild and captive Senegalese sole for optimization of its production under intensive culture conditions.

Selection of housekeeping genes for gene expression studies in larvae from flatfish using real-time PCR

Background

Flatfish metamorphosis involves major physiological and morphological changes. Due to its importance in aquaculture and as a model for developmental studies, some gene expression studies have focused on the understanding of this process using quantitative real-time PCR (qRT-PCR) technique. Therefore, adequate reference genes for accurate normalization are required.

Results

The stability of 12 potential reference genes was examined during larval development in Senegalese sole (Solea senegalensis) and Atlantic halibut (Hippoglossus hippoglossus) to determine the most suitable genes for qRT-PCR analysis. Transcription levels of genes encoding β-Actin (ACTB), glyceraldehyde-3P-dehydrogenase (GAPDH), annexin A2 (ANXA2), glutathione S-transferase (GST), ornithine decarboxylase (ODC), hypoxanthine phosphoribosyltransferase (HPRT1), ubiquitin (UBQ), elongation factor 1 alpha (eEF1A1), 18S ribosomal RNA, and the ribosomal proteins S4 (RPS4) and L13a (RPL13a) were quantitated. Two paralogous genes for ACTB were analyzed in each of both flatfish species. In addition, two paralogous genes for GAPDH were studied in Senegalese sole. RPL13a represented non-orthologous genes between both flatfish species. GeNorm and NormFinder analyses for expression stability revealed RPS4, UBQ and eEF1A1 as the most stable genes in Senegalese sole, Atlantic halibut and in a combined analysis. In all cases, paralogous genes exhibited differences in expression stability.

Conclusion

This work suggests RPS4, UBQ, and eEF1A1 genes as useful reference genes for accurate normalization in qRT-PCR studies in Senegalese sole and Atlantic halibut larvae. The congruent results between both species in spite of the drastic differences in larval development suggest that selected housekeeping genes (HKGs) could be useful in other flatfish species. However, the finding of paralogous gene copies differentially expressed during development in some HKGs underscores the necessity to identify orthologous genes.

Molecular characterization and expression analysis of five different elongation factor 1 alpha genes in the flatfish Senegalese sole (Solea senegalensis Kaup): differential gene expression and thyroid hormones dependence during metamorphosis

BACKGROUND

Eukaryotic elongation factor 1 alpha (eEF1A) is one of the four subunits composing eukaryotic translation elongation factor 1. It catalyzes the binding of aminoacyl-tRNA to the A-site of the ribosome in a GTP-dependent manner during protein synthesis, although it also seems to play a role in other non-translational processes. Currently, little information is still available about its expression profile and regulation during flatfish metamorphosis. With regard to this, Senegalese sole (Solea senegalensis) is a commercially important flatfish in which eEF1A gene remains to be characterized.

RESULTS

The development of large-scale genomics of Senegalese sole has facilitated the identification of five different eEF1A genes, referred to as SseEF1A1, SseEF1A2, SseEF1A3, SseEF1A4, and Sse42Sp50. Main characteristics and sequence identities with other fish and mammalian eEF1As are described. Phylogenetic and tissue expression analyses allowed for the identification of SseEF1A1 and SseEF1A2 as the Senegalese sole counterparts of mammalian eEF1A1 and eEF1A2, respectively, and of Sse42Sp50 as the ortholog of Xenopus laevis and teleost 42Sp50 gene. The other two elongation factors, SseEF1A3 and SseEF1A4, represent novel genes that are mainly expressed in gills and skin. The expression profile of the five genes was also studied during larval development, revealing different behaviours. To study the possible regulation of SseEF1A gene expressions by thyroid hormones (THs), larvae were exposed to the goitrogen thiourea (TU). TU-treated larvae exhibited lower SseEF1A4 mRNA levels than untreated controls at both 11 and 15 days after treatment, whereas transcripts of the other four genes remained relatively unchanged. Moreover, addition of exogenous T4 hormone to TU-treated larvae increased significantly the steady-state levels of SseEF1A4 with respect to untreated controls, demonstrating that its expression is up-regulated by THs.

CONCLUSION

We have identified five different eEF1A genes in the Senegalese sole, referred to as SseEF1A1, SseEF1A2, SseEF1A3, SseEF1A4, and Sse42Sp50. The five genes exhibit different expression patterns in tissues and during larval development. TU and T4 treatments demonstrate that SseEF1A4 is up-regulated by THs, suggesting a role in the translational regulation of the factors involved in the dramatic changes that occurs during Senegalese sole metamorphosis.

Molecular characterization, gene expression and dependence on thyroid hormones of two type I keratin genes (sseKer1 and sseKer2) in the flatfish Senegalese sole (Solea senegalensis Kaup)

BACKGROUND

Keratins make up the largest subgroup of intermediate filaments, and, in chordates, represent the most abundant proteins in epithelial cells. They have been associated with a wide range of functions in the cell, but little information is still available about their expression profile and regulation during flatfish metamorphosis. Senegalese sole (Solea senegalensis) is a commercially important flatfish in which no keratin gene has been described yet.

RESULTS

The development of large-scale genomics of Senegalese sole has facilitated the identification of two different type I keratin genes referred to as sseKer1 and sseKer2. Main characteristics and sequence identities with other fish and mammal keratins are described. Phylogenetic analyses grouped sseKer1 and sseKer2 in a significant clade with other teleost epidermal type I keratins, and have allowed for the identification of sseKer2 as a novel keratin. The expression profile of both genes was studied during larval development and in tissues using a real-time approach. sseKer1 and sseKer2 mRNA levels were significantly higher in skin than in other tissues examined. During metamorphosis, sseKer1 transcripts increased significantly at first stages, and reduced thereafter. In contrast, sseKer2 mRNA levels did not change during early metamorphosis although a significant drop at metamorphosis climax and late metamorphosis was also detected. To study the possible regulation of sseKer gene expressions by thyroid hormones (THs), larvae were exposed to the goitrogen thiourea (TU). TU-treated larvae exhibited higher sseKer1 and sseKer2 mRNA levels than untreated control at both 11 and 15 days after treatment. Moreover, addition of exogenous T4 hormone to TU-treated larvae restored or even reduced the steady-state levels with respect to the untreated control, demonstrating that expression of both genes is negatively regulated by THs.

CONCLUSION

We have identified two keratin genes, referred to as sseKer1 and sseKer2, in Senegalese sole. Phylogenetic analyses revealed sseKer2 as a novel keratin. Although they exhibit different expression patterns during larval development, both of them are negatively regulated by THs. The co-regulation by THs could explain the reduction of both keratin transcripts after the metamorphosis climax, suggesting their role in the tissue remodelling processes that occur during metamorphosis.

Molecular characterization and gene expression of six trypsinogens in the flatfish Senegalese sole (Solea senegalensis Kaup) during larval development and in tissues

The application of large-scale genomics to Senegalese sole (Solea senegalensis) has allowed for the identification of six different trypsinogen genes. The catalytic triad (His-57, Asp-102, and Ser-195) and other residues required for trypsin functionality were conserved across all trypsinogens. Sequence identities, charges and phylogenetic analysis allowed them to be classified into three groups: group I or anionic trypsinogens (ssetryp1a, ssetryp1b and ssetryp1c), group II or cationic trypsinogen (ssetryp2) and group III or psychrophilic trypsinogens (ssetryp3 and ssetrypY). The expression profiles of these genes were studied in juvenile tissues and during larval development using a real-time PCR approach. In juvenile fish, trypsinogens were expressed mainly in the intestine. Transcripts of ssetryp1c were the highest in all tissues except in brain where those of ssetryp2 were the most abundant. During larval development, ssetryp1 variants and ssetryp2 transcript levels increased from 2 to 6 days after hatching, and decreased thereafter. In contrast, transcripts of group III trypsinogens increased slightly or not significantly in premetamorphosis and decreased at metamorphosis. The expression levels ssetryp3 and ssetrypY were the lowest in larvae (from 172- to 1391-fold lower than ssetryp1 and ssetryp2). In contrast, they were expressed at a similar level as ssetryp2, although lower than ssetryp1, in juvenile tissues.