Integration of Transcriptome, Gross Morphology and Histopathology in the Gill of Sea Farmed Atlantic Salmon (Salmo salar): Lessons From Multi-Site Sampling.

The gill of teleost fish is a multifunctional organ involved in many physiological processes such as gas exchange, osmotic and ionic regulation, acid-base balance and excretion of nitrogenous waste. Due to its extensive interface with the environment, the gill plays a key role as a primary mucosal defense tissue against pathogens, as manifested by the presence of the gill-associated lymphoid tissue (GIALT). In recent years, the prevalence of multifactorial gill pathologies has increased significantly, causing substantial losses in Atlantic salmon aquaculture. The transition from healthy to unhealthy gill phenotypes and the progression of multifactorial gill pathologies, such as proliferative gill disease (PGD), proliferative gill inflammation (PGI) and complex gill disorder (CGD), are commonly characterized by epithelial hyperplasia, lamellar fusion and inflammation. Routine monitoring for PGD relies on visual inspection and non-invasive scoring of the gill tissue (gross morphology), coupled with histopathological examination of gill sections. To explore the underlying molecular events that are associated with the progression of PGD, we sampled Atlantic salmon from three different marine production sites in Scotland and examined the gill tissue at three different levels of organization: gross morphology with the use of PGD scores (macroscopic examination), whole transcriptome (gene expression by RNA-seq) and histopathology (microscopic examination). Our results strongly suggested that the changes in PGD scores of the gill tissue were not associated with the changes in gene expression or histopathology. In contrast, integration of the gill RNA-seq data with the gill histopathology enabled us to identify common gene expression patterns associated with multifactorial gill disease, independently from the origin of samples. We demonstrated that the gene expression patterns associated with multifactorial gill disease were dominated by two processes: a range of immune responses driven by pro-inflammatory cytokines and the events associated with tissue damage and repair, driven by caspases and angiogenin.

Dietary Yeast Cell Wall Extract Alters the Proteome of the Skin Mucous Barrier in Atlantic Salmon (Salmo salar): Increased Abundance and Expression of a Calreticulin-Like Protein.

In order to improve fish health and reduce use of chemotherapeutants in aquaculture production, the immunomodulatory effect of various nutritional ingredients has been explored. In salmon, there is evidence that functional feeds can reduce the abundance of sea lice. This study aimed to determine if there were consistent changes in the skin mucus proteome that could serve as a biomarker for dietary yeast cell wall extract. The effect of dietary yeast cell wall extract on the skin mucus proteome of Atlantic salmon was examined using two-dimensional gel electrophoresis. Forty-nine spots showed a statistically significant change in their normalised volumes between the control and yeast cell wall diets. Thirteen spots were successfully identified by peptide fragment fingerprinting and LC-MS/MS and these belonged to a variety of functions and pathways. To assess the validity of the results from the proteome approach, the gene expression of a selection of these proteins was studied in skin mRNA from two different independent feeding trials using yeast cell wall extracts. A calreticulin-like protein increased in abundance at both the protein and transcript level in response to dietary yeast cell wall extract. The calreticulin-like protein was identified as a possible biomarker for yeast-derived functional feeds since it showed the most consistent change in expression in both the mucus proteome and skin transcriptome. The discovery of such a biomarker is expected to quicken the pace of research in the application of yeast cell wall extracts.

Regulatory factors controlling muscle mass: Competition between innate immune function and anabolic signals in regulation of atrogin-1 in Atlantic salmon.

Atrogin-1 is a conserved ubiquitin E3 ligase that is central to the early stages of skeletal and cardiac muscle wasting and degradation following starvation and inflammatory diseases. The control of protein turnover is different between endothermic and ectothermic animals reflecting the body energy requirements. Here we have characterised the promoter of the atrogin-1 gene in a phylogenetically diverse group of vertebrates and show conserved FOXO elements are present in all species examined. We have examined the gene expression responses in primary muscle cell culture to key immune modulators (IL-1ß, interferon type 1 and interferon γ) and to the anabolic hormone insulin like growth factor (IGF-1). We show that the IL-1ß and interferon type 1 increased atrogin-1 mRNA expression whereas IGF-1 suppressed atrogin-1 expression. The proximal promoter of salmon atrogin-1 was used to transfect primary muscle cell cultures and we found all three cytokines increased promoter activity whereas there was a decrease caused by IGF-1 exposure. We hypothesise that the main drivers for atrogin-1 expression are via the conserved FOXO site, but other transcription binding sites such as NFκB, STAT and IRFs may also be involved in a synergistic manner following immune stimulation when free amino acids need to be released for muscle protein reserves.

Antiviral and metabolic gene expression responses to viral infection in Atlantic salmon (Salmo salar).

Salmonid alphavirus (SAV), the aetiological agent of pancreas disease, is recognized as a serious pathogen of farmed Atlantic salmon. This disease results in loss of weight followed by poor growth of surviving fish, as such it is viewed as a wasting disease. SAV and other chronic disease causing viruses affect the heart and skeletal muscle tissues, at present the mechanisms by which pathology occurs is unknown. The relationship between antiviral activity and other physiological parameters especially in skeletal muscle are currently not examined in depth in fish. An experimental SAV (isotype 3) infection was carried out using a cohabitation approach, from which samples were collected at 0, 4, 8 & 12 week post challenge. Maximum viral load in the muscle tissue was 4 weeks post infection which was reduced at 8 weeks and undetectable by 12 weeks. Histopathology score peaked at 4 weeks post infection in pancreas and heart whereas there was maximum damage in skeletal muscle at 8 weeks. The peak expression of antiviral immune genes coincided with the viral load. Several genes involved in protein degradation were increased following infection including atrogin-1 and cathepsin D, at 4 weeks post challenge suggesting reallocation of amino acid reserves. Taken together, these observations increase our understanding of salmon poor growth during viral infection, and will serve as a basis to develop strategies to manage this viral wasting disease.

MULAN related gene (MRG): a potential novel ubiquitin ligase activator of NF-kB involved in immune response in Atlantic salmon (Salmo salar).

Nuclear factor-kB (NF-kB) is a transcription factor that plays a central role in the regulation of a variety of genes including many involved in bacterial and viral infections. NF-kB is normally sequestered by inhibitory proteins (IkBs) in the cytoplasm of non-stimulated cells. The degradation of IkBs by the ubiquitin proteasome pathway releases NF-kB allowing its translocation to the nucleus where it regulates gene transcription. The Mitochondrial Ubiquitin Ligase Activator of NF-kB, (MULAN), is an E3 ubiquitin ligase involved in controlling activation of NF-kB, and regulating mitochondrial dynamics and apoptosis. We report the characterisation of a novel piscine-specific MULAN related gene (MRG) sequence, its mRNA tissue distribution and expression following in vivo and in vitro challenges. MRG cDNA was identified in Atlantic salmon and its sequence encodes a predicted protein of 274 amino acids. The mRNA of MRG was expressed in multiple tissues, with the highest abundance head kidney. An Aeromonas salmonicida bacterial challenge increased expression of this gene in head kidney, liver and gill tissue at 6 h and 24 h. In vitro stimulation of a salmonid cell line indicated MRG was increased in expression following stimulation with LPS, PolyI:C and recombinant trout IL-1ß for 4 h and 24 h. These results suggest an active role of MRG in the activation of the NF-kB pathway during early immune responses.

Transcriptomic and physiological responses to fishmeal substitution with plant proteins in formulated feed in farmed Atlantic salmon (Salmo salar).

BACKGROUND: Aquaculture of piscivorous fish is in continual expansion resulting in a global requirement to reduce the dependence on wild caught fish for generation of fishmeal and fish oil. Plant proteins represent a suitable protein alternative to fish meal and are increasingly being used in fish feed. In this study, we examined the transcriptional response of Atlantic salmon (Salmo salar) to a high marine protein (MP) or low fishmeal, higher plant protein replacement diet (PP), formulated to the same nutritional specification within previously determined acceptable maximum levels of individual plant feed materials. RESULTS: After 77 days of feeding the fish in both groups doubled in weight, however neither growth performance, feed efficiency, condition factor nor organ indices were significantly different. Assessment of histopathological changes in the heart, intestine or liver did not reveal any negative effects of the PP diet. Transcriptomic analysis was performed in mid intestine, liver and skeletal muscle, using an Atlantic salmon oligonucleotide microarray (Salar_2, Agilent 4x44K). The dietary comparison revealed large alteration in gene expression in all the tissues studied between fish on the two diets. Gene ontology analysis showed, in the mid intestine of fish fed PP, higher expression of genes involved in enteritis, protein and energy metabolism, mitochondrial activity/kinases and transport, and a lower expression of genes involved in cell proliferation and apoptosis compared to fish fed MP. The liver of fish fed PP showed a lower expression of immune response genes but a higher expression of cell proliferation and apoptosis processes that may lead to cell reorganization in this tissue. The skeletal muscle of fish fed PP vs MP was characterized by a suppression of processes including immune response, energy and protein metabolism, cell proliferation and apoptosis which may reflect a more energy efficient tissue. CONCLUSIONS: The PP diet resulted in significant effects on transcription in all the 3 tissues studied. Despite of these alterations, we demonstrated that high level of plant derived proteins in a salmon diet allowed fish to grow with equal efficiency as those on a high marine protein diet, and with no difference in biometric quality parameters.

Exploring the transcriptome of Atlantic salmon (Salmo salar) skin, a major defense organ.

The skin of fish is the first line of defense against pathogens and parasites. The skin transcriptome of the Atlantic salmon is poorly characterized, and currently only 2,089 expressed sequence tags (ESTs) out of a total of half a million sequences are generated from skin-derived cDNA libraries. The primary aim of this study was to enhance the transcriptomic knowledge of salmon skin by using next-generation sequencing (NGS) technology, namely the Roche-454 platform. An equimolar mixture of high-quality RNA from skin and epidermal samples of salmon reared in either freshwater or seawater was used for 454-sequencing. This technique yielded over 600,000 reads, which were assembled into 34,696 isotigs using Newbler. Of these isotigs, 12 % had not been sequenced in Atlantic salmon, hence representing previously unreported salmon mRNAs that can potentially be skin-specific. Many full-length genes have been acquired, representing numerous biological processes. Mucin proteins are the main structural component of mucus and we examined in greater detail the sequences we obtained for these genes. Several isotigs exhibited homology to mammalian mucins (MUC2, MUC5AC and MUC5B). Mucin mRNAs are generally >10 kbp and contain large repetitive units, which pose a challenge towards full-length sequence discovery. To date, we have not unearthed any full-length salmon mucin genes with this dataset, but have both N- and C-terminal regions of a mucin type 5. This highlights the fact that, while NGS is indeed a formidable tool for sequence data mining of non-model species, it must be complemented with additional experimental and bioinformatic work to characterize some mRNA sequences with complex features.

Muscle-specific RING finger (MuRF) cDNAs in Atlantic salmon (Salmo salar) and their role as regulators of muscle protein degradation.

The selection of proteins destined for degradation by the ubiquitin-proteasome pathway is coordinated by E3 ubiquitin ligases (E3Ub). One group of E3Ubs is described as muscle-specific RING finger (MuRF) molecules. In mammals, these proteins are believed to be central to targetting of muscle proteins for degradation during physiological perturbations such as starvation and inflammatory responses. In fish, the diversity of MuRF sequences is unexplored as is the expression of their mRNAs. In this study, three MuRF1 cDNAs, denoted as MuRF1a, MuRF1b, and MuRF1c, and a single MuRF2 were identified and characterized in Atlantic salmon. The MuRF1 sequences are highly conserved and encode predicted proteins of 349, 350, and 353 amino acids, whereas MuRF2 encodes a longer protein of 462 amino acids. The evolutionary relationship of these sequences with other fish and mammalian molecules shows that MuRF1a and 1b may have arisen from a recent salmonid duplication. The mRNA of MuRFs was expressed in multiple tissues, with highest abundance in white muscle tissue followed by the heart. The expression of MuRFs was modulated after both starvation and immune challenge. Starvation increased expression of all MuRF mRNAs in white muscle, with the greatest increase found in MuRF1a. A proinflammatory stimulation increased expression of MuRF mRNA in muscle and other tissues indicating a role of these proteins in protein degradation during inflammation.

Cloning and expression analysis of the mitochondrial ubiquitin ligase activator of NF-κB (MULAN) in Atlantic salmon (Salmo salar).

Nuclear factor-κB (NF-κB) is a transcription factor involved in the regulation of a large number of genes including many involved in bacterial and viral infections. NF-κB is normally sequestered by inhibitory proteins (IκBs) in the cytoplasm of non-stimulated cells. The degradation of IκBs by the ubiquitin proteasome pathway leads to the rapid translocation of NF-κB to the nucleous where it regulates gene transcription. The Mitochondrial Ubiquitin Ligase Activator of NF-κB, (MULAN), is an E3 ubiquitin ligase believed to be central in controlling activation of NF-κB, and regulating the mitochondrial dynamics and apoptosis process. We report, for the first time in fish, the characterization of a MULAN cDNA in Atlantic salmon and rainbow trout. The salmonid MULAN sequences encode predicted proteins of 352 amino acids. The mRNA of MULAN was expressed in multiple tissues, with the highest abundance in brain and white muscle. An Aeromonas salmonicida bacterial challenge increased expression of this gene in head kidney, liver and gill both at 6 and at 24h following the infection. In vitro experiments using the salmonid cell line RTG-2 indicated MULAN was increased in expression following 4h stimulation with LPS and recombinant trout IL-1ß. MULAN expression remained increased 24h post-stimulation with both LPS and IL-1ß, but was down regulated by PolyI:C at this time. These results suggest an active role of the MULAN gene in the activation of the NF-κB pathway during piscine immune responses.

Multiple tissue transcriptomic responses to Piscirickettsia salmonis in Atlantic salmon (Salmo salar).

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

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

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

Ubiquitin E3 ligase atrogin-1 (Fbox-32) in Atlantic salmon (Salmo salar): sequence analysis, genomic structure and modulation of expression.

E3 ubiquitin ligases are central for the selection of proteins targeted for degradation by the ubiquitin proteasome pathway. In this study atrogin-1 (Fbox-32), a major E3 ligase in muscle, has been characterized in Atlantic salmon (Salmo salar). The protein sequence is highly conserved between teleosts and mammals and is characterized by the presence of five conserved motifs related to the identification of protein targets. The genomic structure is conserved between teleosts and mammals and contains 9 exon and 8 introns. The phylogenetic relationship between atrogin-1 and two other closely related ubiquitin E3 ligases FBXO25 and MuRF1 showed atrogin-1 and FBXO25 grouped together with MuRF1 being more distant. The mRNAs were expressed in multiple tissues, atrogin-1 and MuRF1 were most abundant in white muscle and heart whereas FBXO25 had greatest expression in brain, white muscle and heart. The transcriptional modulation of these E3 ligases was examined in starved fish and fish following different immune stimulations. Expression of atrogin-1 and MuRF1 was increased following food deprivation, implementing these two genes in degradation of muscle protein during starvation. During viral infection atrogin-1 expression was not altered, whereas it was increased following stimulation with LPS, indicating an onset of catabolic processes during inflammatory responses.

Investigations on the effects of growth rate and dietary vitamin C on skeletal muscle collagen and hydroxylysyl pyridinoline cross-link concentration in farmed Atlantic salmon (Salmo salar).

We have investigated the interactions between dietary vitamin C levels (at 33, 79, 135, and 424 mg kg-1 of wet mass feed) and growth rate on the collagen and cross-link contents of fast muscle in farmed juvenile Atlantic salmon (Salmo salar L.). The growth rate was measured over an 11 week period using the thermal growth coefficient (TGC). Alkaline-soluble (0.1 M NaOH) (a-s) hydroxyproline (HYP) and alkaline-insoluble (i-s) HYP were determined as a measure of collagen content and hydroxylysyl pyridinoline (PYD) as a measure of mature collagen cross-link concentration. There was a approximately 5-fold increase in muscle vitamin C concentration at similar feed conversion ratios ( approximately 0.82) as dietary vitamin C levels increased from 39 to 424 mg kg-1 of wet mass feed. However, even the lowest dietary vitamin C was sufficient for normal skeletal development and growth. The lowest dietary vitamin C level tested resulted in a approximately 27% decrease in the a-sHYP concentration relative to the other diets, whereas there was no significant effect of vitamin C on the i-sHYP and PYD concentrations. ANOVA revealed no significant interaction between vitamin C and growth rate, whereas the covariate TGC was significant for i-sHYP and PYD but not for a-sHYP. Pyridinoline cross-link and i-s HYP concentrations were 11.1 and 7.7% lower, respectively, in high (TGC > 3.9) mass than low (TGC < 3.9) growth rate fish. These small differences in collagen cross-linking were associated with a 15.6% decrease in fillet firmness measured with an instrumental texture analyzer. It was concluded that for healthy juvenile salmon reared under controlled growth conditions, the dietary vitamin C inclusion of 79 mg kg-1 of wet mass feed was sufficient to produce the required synthesis of soluble muscle collagen. Furthermore, post-translational modifications of the collagen leading to cross-linking showed a small decrease with increasing growth rate but was independent of vitamin C concentration in the diet at these levels.

Hydroxylysyl pyridinoline cross-link concentration affects the textural properties of fresh and smoked Atlantic salmon (Salmo salar L.) flesh.

A simple HPLC method is presented to quantify the low concentration of hydroxylysyl pyridinoline (PYD) cross-links in Atlantic salmon (Salmo salar L.) muscle. The method involved the extraction of tissue with NaOH prior to hydrolysis, which greatly reduced the amount of protein to be hydrolyzed and made downstream operations easier and more reproducible. The concentration of PYD was 426 pmol g(-)(1) dry mass muscle in post-rigor muscle stored at 0 degrees C and sampled 3 d after death. Hydroxproline (HYP) concentration was determined following NaOH extraction as a measure of collagen content. In post-rigor samples, the alkaline-insoluble HYP fraction comprised 18.3% of the total HYP. Scanning electron microscopy revealed shrinkage of muscle fibers and a retraction of the connective tissue matrix in smoked salmon. PYD concentration was relatively resistant to processing to the smoked product, decreasing by around 11.7%, as compared to a 22.2% decrease in HYP. There was a positive correlation between PYD concentration and the firmness of post-rigor muscle samples as measured by an instrumental texture analyzer, explaining 25% of the total variation. A weaker but still significant correlation was found between PYD concentration and firmness in the smoked product. There was no relationship between fillet firmness and total collagen concentration, although the correlation with HYP in the alkaline-insoluble fraction was significant at the 6% level (P = 0.057). Our results indicate that only 1-3% of collagen molecules are linked by nonreducible mature cross-links in harvest size farmed Atlantic salmon and that PYD concentration is an important raw material characteristic for flesh quality.