Molecular characterization of muscle atrophy and proteolysis associated with spawning in rainbow trout

Integrated Analyses of DNA Methylation and Gene Expression of Rainbow Trout Muscle under Variable Ploidy and Muscle Atrophy Conditions

Rainbow trout, Oncorhynchus mykiss, is an important cool, freshwater aquaculture species used as a model for biological research. However, its genome reference has not been annotated for epigenetic markers affecting various biological processes, including muscle growth/atrophy. Increased energetic demands during gonadogenesis/reproduction provoke muscle atrophy in rainbow trout. We described DNA methylation and its associated gene expression in atrophying muscle by comparing gravid, diploid females to sterile, triploid females. Methyl Mini-seq and RNA-Seq were simultaneously used to characterize genome-wide DNA methylation and its association with gene expression in rainbow trout muscle. Genome-wide enrichment in the number of CpGs, accompanied by depleted methylation levels, was noticed around the gene transcription start site (TSS). Hypermethylation of CpG sites within ±1 kb on both sides of TSS (promoter and gene body) was weakly/moderately associated with reduced gene expression. Conversely, hypermethylation of the CpG sites in downstream regions of the gene body +2 to +10 kb was weakly associated with increased gene expression. Unlike mammalian genomes, rainbow trout gene promotors are poor in CpG islands, at <1% compared to 60%. No signs of genome-wide, differentially methylated (DM) CpGs were observed due to the polyploidy effect; only 1206 CpGs (0.03%) were differentially methylated, and these were primarily associated with muscle atrophy. Twenty-eight genes exhibited differential gene expression consistent with methylation levels of 31 DM CpGs. These 31 DM CpGs represent potential epigenetic markers of muscle atrophy in rainbow trout. The DM CpG-harboring genes are involved in apoptosis, epigenetic regulation, autophagy, collagen metabolism, cell membrane functions, and Homeobox proteins. Our study also identified genes explaining higher water content and modulated glycolysis previously shown as characteristic biochemical signs of rainbow trout muscle atrophy associated with sexual maturation. This study characterized DNA methylation in the rainbow trout genome and its correlation with gene expression. This work also identified novel epigenetic markers associated with muscle atrophy in fish/lower vertebrates.

Gene expression profiling of trout muscle during flesh quality recovery following spawning

Background

Sexual maturation causes loss of fish muscle mass and deterioration of fillet quality attributes that prevent market success. We recently showed that fillet yield and flesh quality recover in female trout after spawning. To gain insight into the molecular mechanisms regulating flesh quality recovery, we used an Agilent-based microarray platform to conduct a large-scale time course analysis of gene expression in female trout white muscle from spawning to 33 weeks post-spawning.

Results

In sharp contrast to the situation at spawning, muscle transcriptome of female trout at 33 weeks after spawning was highly similar to that of female trout of the same cohort that did not spawn, which is consistent with the post-spawning flesh quality recovery. Large-scale time course analysis of gene expression in trout muscle during flesh quality recovery following spawning led to the identification of approximately 3340 unique differentially expressed genes that segregated into four major clusters with distinct temporal expression profiles and functional categories. The first cluster contained approximately 1350 genes with high expression at spawning and downregulation after spawning and was enriched with genes linked to mitochondrial ATP synthesis, fatty acid catabolism and proteolysis. A second cluster of approximately 540 genes with transient upregulation 2 to 8 weeks after spawning was enriched with genes involved in transcription, RNA processing, translation, ribosome biogenesis and protein folding. A third cluster containing approximately 300 genes upregulated 4 to 13 weeks after spawning was enriched with genes encoding ribosomal subunits or regulating protein folding. Finally, a fourth cluster that contained approximately 940 genes with upregulation 8 to 24 weeks after spawning, was dominated by genes encoding myofibrillar proteins and extracellular matrix components and genes involved in glycolysis.

Conclusion

Overall, our study indicates that white muscle tissue restoration and flesh quality recovery after spawning are associated with transcriptional changes promoting anaerobic ATP production, muscle fibre hypertrophic growth and extracellular matrix remodelling. The generation of the first database of genes associated with post-spawning muscle recovery may provide insights into the molecular and cellular mechanisms controlling muscle yield and fillet quality in fish and provide a useful list of potential genetic markers for these traits.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08228-3.

Endoplasmic reticulum stress as a key mechanism in stunted growth of seawater rainbow trout (Oncorhynchus mykiss)

BACKGROUND

Rainbow trout (Oncorhynchus mykiss) is a salmonid species with a complex life-history. Wild populations are naturally divided into freshwater residents and sea-run migrants. Migrants undergo an energy-demanding adaptation for life in seawater, known as smoltification, while freshwater residents display these changes in an attenuated magnitude and rate. Despite this, in seawater rainbow trout farming all fish are transferred to seawater. Under these circumstances, weeks after seawater transfer, a significant portion of the fish die (around 10%) or experience growth stunting (GS; around 10%), which represents an important profitability and welfare issue. The underlying causes leading to GS in seawater-transferred rainbow trout remain unknown. In this study, we aimed at characterising the GS phenotype in seawater-transferred rainbow trout using untargeted and targeted approaches. To this end, the liver proteome (LC-MS/MS) and lipidome (LC-MS) of GS and fast-growing phenotypes were profiled to identify molecules and processes that are characteristic of the GS phenotype. Moreover, the transcription, abundance or activity of key proteins and hormones related to osmoregulation (Gill Na+, K + -ATPase activity), growth (plasma IGF-I, and liver igf1, igfbp1b, ghr1 and ctsl) and stress (plasma cortisol) were measured using targeted approaches.

RESULTS

No differences in Gill Na+, K + -ATPase activity and plasma cortisol were detected between the two groups. However, a significant downregulation in plasma IGF-I and liver igf1 transcription pointed at this growth factor as an important pathomechanism for GS. Changes in the liver proteome revealed reactive-oxygen-species-mediated endoplasmic reticulum stress as a key mechanism underlying the GS phenotype. From the lipidomic analysis, key observations include a reduction in triacylglycerols and elevated amounts of cardiolipins, a characteristic lipid class associated with oxidative stress, in GS phenotype.

CONCLUSION

While the triggers to the activation of endoplasmic reticulum stress are still unknown, data from this study point towards a nutritional deficiency as an underlying driver of this phenotype.

Distinct microbial assemblages associated with genetic selection for high- and low- muscle yield in rainbow trout

Background

Fish gut microbial assemblages play a crucial role in the growth rate, metabolism, and immunity of the host. We hypothesized that the gut microbiota of rainbow trout was correlated with breeding program based genetic selection for muscle yield. To test this hypothesis, fecal samples from 19 fish representing an F2 high-muscle genetic line (ARS-FY-H) and 20 fish representing an F1 low-muscle yield genetic line (ARS-FY-L) were chosen for microbiota profiling using the 16S rRNA gene. Significant differences in microbial assemblages between these two genetic lines might represent the effect of host genetic selection in structuring the gut microbiota of the host.

Results

Tukey’s transformed inverse Simpson indices indicated that high muscle yield genetic line (ARS-FY-H) samples have higher microbial diversity compared to those of the low muscle yield genetic line (ARS-FY-L) (LMM, χ2(1) =14.11, p < 0.05). The fecal samples showed statistically distinct structure in microbial assemblages between the genetic lines (F_1,36 = 4.7, p < 0.05, R² = 11.9%). Functional profiling of bacterial operational taxonomic units predicted characteristic functional capabilities of the microbial communities in the high (ARS-FY-H) and low (ARS-FY-L) muscle yield genetic line samples.

Conclusion

The significant differences of the microbial assemblages between high (ARS-FY-H) and low (ARS-FY-L) muscle yield genetic lines indicate a possible effect of genetic selection on the microbial diversity of the host. The functional composition of taxa demonstrates a correlation between bacteria and improving the muscle accretion in the host, probably, by producing various metabolites and enzymes that might aid in digestion. Further research is required to elucidate the mechanisms involved in shaping the microbial community through host genetic selection.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-020-07204-7.

Effect of dietary selenium on postprandial protein deposition in the muscle of juvenile rainbow trout (Oncorhynchus mykiss)

Se, an essential biological trace element, is required for fish growth. However, the underlying mechanisms remain unclear. Protein deposition in muscle is an important determinant for fish growth. This study was conducted on juvenile rainbow trout (Oncorhynchus mykiss) to explore the nutritional effects of Se on protein deposition in fish muscle by analysing the postprandial dynamics of both protein synthesis and protein degradation. Trout were fed a basal diet supplemented with or without 4 mg/kg Se (as Se yeast), which has been previously demonstrated as the optimal supplemental level for rainbow trout growth. After 6 weeks of feeding, dietary Se supplementation exerted no influence on fish feed intake, whereas it increased fish growth rate, feed efficiency, protein retention rate and muscle protein content. Results of postprandial dynamics (within 24 h after feeding) of protein synthesis and degradation in trout muscle showed that dietary Se supplementation led to a persistently hyperactivated target of rapamycin complex 1 pathway and the suppressive expression of numerous genes related to the ubiquitin-proteasome system and the autophagy-lysosome system after the feeding. However, the ubiquitinated proteins and microtubule-associated light chain 3B (LC3)-II:LC3-I ratio, biomarkers for ubiquitination and autophagy activities, respectively, exhibited no significant differences among the fish fed different experimental diets throughout the whole postprandial period. Overall, this study demonstrated a promoting effect of nutritional level of dietary Se on protein deposition in fish muscle by accelerating postprandial protein synthesis. These results provide important insights about the regulatory role of dietary Se in fish growth.

Genome-wide scan for common variants associated with intramuscular fat and moisture content in rainbow trout

BACKGROUND

Genetic improvement of fillet quality attributes is a priority of the aquaculture industry. Muscle composition impacts quality attributes such as flavor, appearance, texture, and juiciness. Fat and moisture make up about ~ 80% of the tissue weight. The genetic architecture underlying the fat and moisture content of the muscle is still to be fully explored in fish. A 50 K gene transcribed SNP chip was used for genotyping 789 fish with available phenotypic data for fat and moisture content. Genotyped fish were obtained from two consecutive generations produced in the National Center for Cool and Cold Water Aquaculture (NCCCWA) growth-selective breeding program. Estimates of SNP effects from weighted single-step GBLUP (WssGBLUP) were used to perform genome-wide association (GWA) analysis to identify quantitative trait loci (QTL) associated with the studied traits.

RESULTS

Using genomic sliding windows of 50 adjacent SNPs, 137 and 178 SNPs were identified as associated with fat and moisture content, respectively. Chromosomes 19 and 29 harbored the highest number of SNPs explaining at least 2% of the genetic variation in fat and moisture content. A total of 61 common SNPs on chromosomes 19 and 29 affected the aforementioned traits; this association suggests common mechanisms underlying intramuscular fat and moisture content. Additionally, based on single-marker GWA analyses, 8 and 24 SNPs were identified in association with fat and moisture content, respectively.

CONCLUSION

SNP-harboring genes were primarily involved in lipid metabolism, cytoskeleton remodeling, and protein turnover. This work provides putative SNP markers that could be prioritized and used for genomic selection in breeding programs.

Genome-Wide Association Analysis With a 50K Transcribed Gene SNP-Chip Identifies QTL Affecting Muscle Yield in Rainbow Trout

Detection of coding/functional SNPs that change the biological function of a gene may lead to identification of putative causative alleles within QTL regions and discovery of genetic markers with large effects on phenotypes. This study has two-fold objectives, first to develop, and validate a 50K transcribed gene SNP-chip using RNA-Seq data. To achieve this objective, two bioinformatics pipelines, GATK and SAMtools, were used to identify ~21K transcribed SNPs with allelic imbalances associated with important aquaculture production traits including body weight, muscle yield, muscle fat content, shear force, and whiteness in addition to resistance/susceptibility to bacterial cold-water disease (BCWD). SNPs ere identified from pooled RNA-Seq data collected from ~620 fish, representing 98 families from growth- and 54 families from BCWD-selected lines with divergent phenotypes. In addition, ~29K transcribed SNPs without allelic-imbalances were strategically added to build a 50K Affymetrix SNP-chip. SNPs selected included two SNPs per gene from 14K genes and ~5K non-synonymous SNPs. The SNP-chip was used to genotype 1728 fish. The average SNP calling-rate for samples passing quality control (QC; 1,641 fish) was ≥ 98.5%. The second objective of this study was to test the feasibility of using the new SNP-chip in GWA (Genome-wide association) analysis to identify QTL explaining muscle yield variance. GWA study on 878 fish (representing 197 families from 2 consecutive generations) with muscle yield phenotypes and genotyped for 35K polymorphic markers (passing QC) identified several QTL regions explaining together up to 28.40% of the additive genetic variance for muscle yield in this rainbow trout population. The most significant QTLs were on chromosomes 14 and 16 with 12.71 and 10.49% of the genetic variance, respectively. Many of the annotated genes in the QTL regions were previously reported as important regulators of muscle development and cell signaling. No major QTLs were identified in a previous GWA study using a 57K genomic SNP chip on the same fish population. These results indicate improved detection power of the transcribed gene SNP-chip in the target trait and population, allowing identification of large-effect QTLs for important traits in rainbow trout.

Crosstalk among lncRNAs, microRNAs and mRNAs in the muscle 'degradome' of rainbow trout

In fish, protein-coding and noncoding genes involved in muscle atrophy are not fully characterized. In this study, we characterized coding and noncoding genes involved in gonadogenesis-associated muscle atrophy, and investigated the potential functional interplay between these genes. Using RNA-Seq, we compared expression pattern of mRNAs, long noncoding RNAs (lncRNAs) and microRNAs of atrophying skeletal muscle from gravid females and control skeletal muscle from age-matched sterile individuals. A total of 852 mRNAs, 1,160 lncRNAs and 28 microRNAs were differentially expressed (DE) between the two groups. Muscle atrophy appears to be mediated by many genes encoding ubiquitin-proteasome system, autophagy related proteases, lysosomal proteases and transcription factors. Transcripts encoding atrogin-1 and mir-29 showed exceptional high expression in atrophying muscle, suggesting an important role in bulk muscle proteolysis. DE genes were co-localized in the genome with strong expression correlation, and they exhibited extensive 'lncRNA-mRNA', 'lncRNA-microRNA', 'mRNA-microRNA' and 'lncRNA-protein' physical interactions. DE genes exhibiting potential functional interactions comprised the highly correlated 'lncRNA-mRNA-microRNA' gene network described as 'degradome'. This study pinpoints extensive coding and noncoding RNA interactions during muscle atrophy in fish, and provides valuable resources for future mechanistic studies.

Comprehensive analysis of lncRNAs and mRNAs in skeletal muscle of rainbow trout (Oncorhynchus mykiss) exposed to estradiol

Estradiol (E2) is a steroid hormone that negatively affects muscle growth in rainbow trout (Oncorhynchus mykiss), but the mechanisms directing with this response are not fully understood. To better characterize the effects of E2 in muscle, we identified differentially regulated mRNAs and lncRNAs in juvenile rainbow trout exposed to E2. Here, we performed next-generation RNA sequencing and comprehensive bioinformatics analyses to characterize the transcriptome profiles, including mRNAs and long noncoding RNAs (lncRNAs), in skeletal muscle of rainbow trout injected with E2. A total of 226 lncRNAs and 253 mRNAs were identified as differentially regulated. We identified crucial pathways, including several signal transduction pathways, hormone response, oxidative response and protein, carbon and fatty acid metabolism pathways. Subsequently, a functional lncRNA-mRNA co-expression network was constructed, which consisted of 681 co-expression relationships between 164 lncRNAs and 201 mRNAs. Moreover, a lncRNA-pathway network was constructed. A total of 65 key lncRNAs were identified that regulate 20 significantly enriched pathways. Overall, our analysis provides insights into mRNA and lncRNA networks in rainbow trout skeletal muscle and their regulation by E2 while understanding the molecular mechanism of lncRNAs.

Identification of SNPs associated with muscle yield and quality traits using allelic-imbalance analyses of pooled RNA-Seq samples in rainbow trout

Background

Coding/functional SNPs change the biological function of a gene and, therefore, could serve as “large-effect” genetic markers. In this study, we used two bioinformatics pipelines, GATK and SAMtools, for discovering coding/functional SNPs with allelic-imbalances associated with total body weight, muscle yield, muscle fat content, shear force, and whiteness. Phenotypic data were collected for approximately 500 fish, representing 98 families (5 fish/family), from a growth-selected line, and the muscle transcriptome was sequenced from 22 families with divergent phenotypes (4 low- versus 4 high-ranked families per trait).

Results

GATK detected 59,112 putative SNPs; of these SNPs, 4798 showed allelic imbalances (>2.0 as an amplification and <0.5 as loss of heterozygosity). SAMtools detected 87,066 putative SNPs; and of them, 4962 had allelic imbalances between the low- and high-ranked families. Only 1829 SNPs with allelic imbalances were common between the two datasets, indicating significant differences in algorithms. The two datasets contained 7930 non-redundant SNPs of which 4439 mapped to 1498 protein-coding genes (with 6.4% non-synonymous SNPs) and 684 mapped to 295 lncRNAs. Validation of a subset of 92 SNPs revealed 1) 86.7–93.8% success rate in calling polymorphic SNPs and 2) 95.4% consistent matching between DNA and cDNA genotypes indicating a high rate of identifying SNPs with allelic imbalances. In addition, 4.64% SNPs revealed random monoallelic expression. Genome distribution of the SNPs with allelic imbalances exhibited high density for all five traits in several chromosomes, especially chromosome 9, 20 and 28. Most of the SNP-harboring genes were assigned to important growth-related metabolic pathways.

Conclusion

These results demonstrate utility of RNA-Seq in assessing phenotype-associated allelic imbalances in pooled RNA-Seq samples. The SNPs identified in this study were included in a new SNP-Chip design (available from Affymetrix) for genomic and genetic analyses in rainbow trout.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3992-z) contains supplementary material, which is available to authorized users.

Estradiol regulates expression of miRNAs associated with myogenesis in rainbow trout

17β-Estradiol (E2) is a steroid hormone that negatively affects muscle growth in rainbow trout, but the mechanism associated with this response is not fully understood. To better characterize the effects of E2 on muscle, we identified differentially regulated microRNAs (miRNAs) and muscle atrophy-related transcripts in juvenile rainbow trout exposed to E2. Small RNA-Seq analysis of E2-treated vs. control muscle identified 36 differentially expressed miRNAs including those known to be involved in myogenesis, cell cycle, apoptosis, and cell death. Some important myogenic miRNAs, such as miR-133 and miR-206, are upregulated while others like miR-145 and miR-499, are downregulated. Gene Ontology analysis of the target genes regulated by the miRNAs involved in atrophy and cell cycle indicates that E2 influence leads to expansion of quiescent myogenic precursor cell population to address atrophying mature muscle in rainbow trout during sexual development.

Characterisation and expression analysis of cathepsins and ubiquitin-proteasome genes in gilthead sea bream (Sparus aurata) skeletal muscle

Background

The proteolytic enzymes involved in normal protein turnover in fish muscle are also responsible for post-mortem softening of the flesh and are therefore potential determinants of product quality. The main enzyme systems involved are calpains, cathepsins, and the ubiquitin-proteasome (UbP). In this study on Sparus aurata (Sa), the coding sequences of cathepsins (SaCTSB and SaCTSDb) and UbP family members (SaN3 and SaUb) were cloned from fast skeletal muscle, and their expression patterns were examined during ontogeny and in a fasting/re-feeding experiment.

Results

The amino acid sequences identified shared 66-100% overall identity with their orthologues in other vertebrates, with well conserved characteristic functional domains and catalytic residues. SaCTSDb showed phylogenetic, sequence and tissue distribution differences with respect to its paralogue SaCTSDa, previously identified in the ovary. Expression of gilthead sea bream cathepsins (B, L, Da, Db) and UbP members (N3, Ub, MuRF1 and MAFbx) in fast skeletal muscle was determined at three different life-history stages and in response to fasting and re-feeding in juveniles. Most of the proteolytic genes analysed were significantly up-regulated during fasting, and down-regulated with re-feeding and, between the fingerling (15 g) and juvenile/adult stages (~50/500 g), consistent with a decrease in muscle proteolysis in both later contexts. In contrast, SaCTSDa and SaMuRF1 expression was relatively stable with ontogeny and SaUb had higher expression in fingerlings and adults than juveniles.

Conclusions

The data obtained in the present study suggest that cathepsins and UbP genes in gilthead sea bream are co-ordinately regulated during ontogeny to control muscle growth, and indicate that feeding regimes can modulate their expression, providing a potential dietary method of influencing post-mortem fillet tenderisation, and hence, product quality.

Electronic supplementary material

The online version of this article (doi:10.1186/s13104-015-1121-0) contains supplementary material, which is available to authorized users.

Comparison of growth-related traits and gene expression profiles between the offspring of neomale (XX) and normal male (XY) rainbow trout

All-female lines of fish are created by crossing sex reversed (XX genotype) males with normal females. All-female lines avoid the deleterious phenotypic effects that are typical of precocious maturation in males. To determine whether all-female and mixed sex populations of rainbow trout (Oncorhynchus mykiss) differ in performance, we compared the growth and gene expression profiles in progeny groups produced by crossing a XX male and a XY male to the same five females. Body weight and length were measured in the resulting all-female (XX) and mixed sex (XX/XY) offspring groups. Microarray experiments with liver and white muscle were used to determine if the gene expression profiles of large and small XX offspring differ from those in large and small XX/XY offspring. We detected no significant differences in body length and weight between offspring groups but XX offspring were significantly less variable in the value of these traits. A large number of upregulated genes were shared between the large XX and large XX/XY offspring; the small XX and small XX/XY offspring also shared similar expression profiles. No GO category differences were seen in the liver or between the large XX and large XX/XY offspring in the muscle. The greatest differences between the small XX and small XX/XY offspring were in the genes assigned to the "small molecule metabolic process" and "cellular metabolic process" GO level 3 categories. Similarly, genes within these categories as well as the category "macromolecule metabolic process" were more highly expressed in small compared to large XX fish.

The concentration of plasma metabolites varies throughout reproduction and affects offspring number in wild brown trout (Salmo trutta)

In wild populations, measuring energy invested in the reproduction and disentangling investment in gametes versus investment in reproductive behavior (such as intrasexual competition or intersexual preference) remain challenging. In this study, we investigated the energy expenditure in brown trout reproductive behavior by using two proxies: variation in weight and variation of plasma metabolites involved in energy production, over the course of reproductive season in a semi natural experimental river. We estimated overall reproductive success using genetic assignment at the end of the reproductive season. Results show that triglycerides and free fatty acid concentrations vary negatively during reproduction, while amino-acids and glucose concentrations remain stable. Decrease in triglyceride and free fatty acid concentrations during reproduction is not related to initial concentration levels or to weight variation. Both metabolite concentration variations and weight variations are correlated to the number of offspring produced, which could indicate that gametic and behavioral reproductive investments substantially contribute to reproductive success in wild brown trout. This study opens a path to further investigate variations in reproductive investment in wild populations.

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

Background

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

Methods and Findings

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

Conclusions

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

Differential gene expression in small and large rainbow trout derived from two seasonal spawning groups

Background

Growth in fishes is regulated via many environmental and physiological factors and is shaped by the genetic background of each individual. Previous microarray studies of salmonid growth have examined fish experiencing either muscle wastage or accelerated growth patterns following refeeding, or the influence of growth hormone and transgenesis. This study determines the gene expression profiles of genetically unmanipulated large and small fish from a domesticated salmonid strain reared on a typical feeding regime. Gene expression profiles of white muscle and liver from rainbow trout (Oncorhynchus mykiss) from two seasonal spawning groups (September and December lots) within a single strain were examined when the fish were 15 months of age to assess the influence of season (late fall vs. onset of spring) and body size (large vs. small).

Results

Although IGFBP1 gene expression was up-regulated in the livers of small fish in both seasonal lots, few expression differences were detected in the liver overall. Faster growing Dec. fish showed a greater number of differences in white muscle expression compared to Sept. fish. Significant differences in the GO Generic Level 3 categories ‘response to external stimulus’, ‘establishment of localization’, and ‘response to stress’ were detected in white muscle tissue between large and small fish. Larger fish showed up-regulation of cytoskeletal component genes while many genes related to myofibril components of muscle tissue were up-regulated in small fish. Most of the genes up-regulated in large fish within the ‘response to stress’ category are involved in immunity while in small fish most of these gene functions are related to apoptosis.

Conclusions

A higher proportion of genes in white muscle compared to liver showed similar patterns of up- or down-regulation within the same size class across seasons supporting their utility as biomarkers for growth in rainbow trout. Differences between large and small Sept. fish in the ‘response to stress’ and ‘response to external stimulus’ categories for white muscle tissue, suggests that smaller fish have a greater inability to handle stress compared to the large fish. Sampling season had a significant impact on the expression of genes related to the growth process in rainbow trout.

Effect of sexual maturation on muscle gene expression of rainbow trout: RNA-Seq approach

Muscle degradation occurs as a response to various physiological states that are regulated by specific molecular mechanisms. Previously, we characterized the metabolic changes of muscle deterioration of the female rainbow trout at full sexual maturity and spawning (Salem et al., Physiol. Genomics 2006;28:33–45; J. Proteomics 2010;73:778–789). Muscle deterioration in this model represents nutrient mobilization as a response to the energetic overdemands of the egg/ovarian growth phase. Our recent studies showed that most of the changes in muscle growth and quality start 2–3 months before spawning. Gravid fish exhibited reduced intramuscular fat that is lower in saturated and monounsaturated fatty acids and higher in polyunsaturated fatty acids compared to sterile fish. In this study, RNA-Seq was used to explain the mechanisms underlying changes during this phase of sexual maturity. Furthermore, to minimize changes due to nutrient deficits, fish were fed on a high-plane of nutrition. The RNA-Seq technique identified a gene expression signature that is consistent with metabolic changes of gravid fish. Gravid fish exhibited increased abundance of transcripts in metabolic pathways of fatty acid degradation and up-regulated expression of genes involved in biosynthesis of unsaturated fatty acids. In addition, increased expression of genes involved in the citric acid cycle and oxidative phosphorylation was observed for gravid fish. This muscle transcriptomic signature of fish fed on a high nutritional plane is quite distinct from that previously described for fish at terminal stages of maturity and suggest that female rainbow trout approaching spawning, on high nutritional planes, likely mobilize intramuscular fat rather than protein to support gonadal maturation.

Deep RNA sequencing of the skeletal muscle transcriptome in swimming fish

Deep RNA sequencing (RNA-seq) was performed to provide an in-depth view of the transcriptome of red and white skeletal muscle of exercised and non-exercised rainbow trout (Oncorhynchus mykiss) with the specific objective to identify expressed genes and quantify the transcriptomic effects of swimming-induced exercise. Pubertal autumn-spawning seawater-raised female rainbow trout were rested (n = 10) or swum (n = 10) for 1176 km at 0.75 body-lengths per second in a 6,000-L swim-flume under reproductive conditions for 40 days. Red and white muscle RNA of exercised and non-exercised fish (4 lanes) was sequenced and resulted in 15–17 million reads per lane that, after de novo assembly, yielded 149,159 red and 118,572 white muscle contigs. Most contigs were annotated using an iterative homology search strategy against salmonid ESTs, the zebrafish Danio rerio genome and general Metazoan genes. When selecting for large contigs (>500 nucleotides), a number of novel rainbow trout gene sequences were identified in this study: 1,085 and 1,228 novel gene sequences for red and white muscle, respectively, which included a number of important molecules for skeletal muscle function. Transcriptomic analysis revealed that sustained swimming increased transcriptional activity in skeletal muscle and specifically an up-regulation of genes involved in muscle growth and developmental processes in white muscle. The unique collection of transcripts will contribute to our understanding of red and white muscle physiology, specifically during the long-term reproductive migration of salmonids.

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.

Generation of a reference transcriptome for evaluating rainbow trout responses to various stressors

Background

Fish under intensive culture conditions are exposed to a variety of acute and chronic stressors, including high rearing densities, sub-optimal water quality, and severe thermal fluctuations. Such stressors are inherent in aquaculture production and can induce physiological responses with adverse effects on traits important to producers and consumers, including those associated with growth, nutrition, reproduction, immune response, and fillet quality. Understanding and monitoring the biological mechanisms underlying stress responses will facilitate alleviating their negative effects through selective breeding and changes in management practices, resulting in improved animal welfare and production efficiency.

Results

Physiological responses to five treatments associated with stress were characterized by measuring plasma lysozyme activity, glucose, lactate, chloride, and cortisol concentrations, in addition to stress-associated transcripts by quantitative PCR. Results indicate that the fish had significant stressor-specific changes in their physiological conditions. Sequencing of a pooled normalized transcriptome library created from gill, brain, liver, spleen, kidney and muscle RNA of control and stressed fish produced 3,160,306 expressed sequence tags which were assembled and annotated. SNP discovery resulted in identification of ~58,000 putative single nucleotide polymorphisms including 24,479 which were predicted to fall within exons. Of these, 4907 were predicted to occupy the first position of a codon and 4110 the second, increasing the probability to impact amino acid sequence variation and potentially gene function.

Conclusion

We have generated and characterized a reference transcriptome for rainbow trout that represents multiple tissues responding to multiple stressors common to aquaculture production environments. This resource compliments existing public transcriptome data and will facilitate approaches aiming to evaluate gene expression associated with stress in this species.

Effects of sex steroids on indices of protein turnover in rainbow trout (Oncorhynchusmykiss) white muscle

Effects of 17β-estradiol (E2), testosterone, and 5α-dihydrotestosterone (DHT) on protein turnover and proteolytic gene expression were determined in rainbow trout (Oncorhynchus mykiss) primary myocytes and white muscle tissue. E2 reduced rates of protein synthesis and increased rates of protein degradation in primary myocytes by 45% and 27%, respectively. DHT reduced rates of protein synthesis by 27%. Testosterone did not affect protein synthesis and neither testosterone nor DHT affected rates of protein degradation. Single injections of E2 increased expression of ubiquitin ligase genes fbxo32, fbxo25, and murf1, and the proteasome subunit psmd6 by 24h after injection. Within the cathepsin-lysosome pathway, E2 increased expression of cathepsins ctsd and ctsl, as well as autophagy-related genes atg4b and lc3b. Additionally, E2 injection up-regulated the expression of casp3 and casp9 caspase genes. Incubation of primary myocytes with E2 also increased expression of ubiquitin ligase genes. Therefore, catabolic effects of E2 on protein turnover result in part from E2-induced increases in proteolytic gene expression directly in muscle. Injection of testosterone increased milli-calpain (capn2) and casp3 expression, and DHT increased ctsd expression in vivo, whereas both androgens up-regulated fbxo32 expression in primary myocytes. These results suggest that effects of androgens on protein turnover in muscle are not driven primarily by direct effects of these hormones in this tissue.

Molecular characterization of the MuRF genes in rainbow trout: Potential role in muscle degradation

Muscle growth is determined primarily by the balance between protein synthesis and degradation. When rates of protein synthesis are similar between individuals, protein degradation is critical in explaining differences in growth efficiency. Studies in mammals showed that muscle atrophy results from increased protein breakdown, and is associated with activation of the ubiquitin proteasome pathway, including induction of the muscle-specific ubiquitin protein ligase, MuRF1. Animals lacking MuRF1 are resistant to muscle atrophy. In fish, little is known about the role of the proteasome/MuRF pathway in muscle degradation. The objectives of this study were to: 1) clone and characterize MuRF genes in rainbow trout; and 2) determine expression of MuRF genes in association with starvation- and vitellogenesis-induced muscle atrophy in rainbow trout. We have identified full-length cDNA sequences for three MuRF genes (MuRF1, MuRF2, and MuRF3). These genes encode proteins with typical MuRF structural domains, including a RING-finger, a B-box and a Leucine-rich coiled-coil domain. RT-PCR analysis showed that MuRF genes are predominantly expressed in muscle and heart tissues. Real time PCR analysis revealed that expression of all MuRF genes is up-regulated during starvation and MuRF3 is up-regulated in vitellogenesis-associated muscle degradation. These results suggest that MuRF genes have an important role in fish muscle protein degradation. Further studies are warranted to assess the potential use of MuRF genes as tools to monitor fish muscle growth and degradation.

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

BACKGROUND

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

RESULTS

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

CONCLUSIONS

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

Gene expression profiling and environmental contaminant assessment of migrating Pacific salmon in the Fraser River watershed of British Columbia

The health and physiological condition of anadromous salmon is of concern as their upriver migration requires navigation of human-impacted waterways and metabolism of stored energy reserves containing anthropogenic contaminants. Such factors may affect reproductive success of fish stocks. This study investigates chemical contaminant burdens and select gene expression profiles in Pacific Sockeye (Oncorhynchus nerka) and Chinook (Oncorhynchus tshawytscha) salmon which traverse the Fraser River watershed during their spawning migration. Chemical analyses of muscle tissue and eggs of salmon collected from the lower Fraser River (pre-migration) and from upstream spawning grounds (post-migration) during the 2007 migration revealed the presence of numerous chemical contaminants, including PCBs, dioxins/furans, pesticides, and heavy metals. However, muscle tissue residue concentrations were well below human health consumption guidelines and 2,3,7,8 TCDD toxic equivalents (SigmaTEQs) in salmon eggs, calculated using WHO toxic equivalency factors (WHO-TEFs) for fish health, did not exceed the 0.3pgg(-1) wet weight toxicological threshold level previously associated with 30% egg mortality in salmon populations. Quantitative real-time PCR probes were generated and used to assess differences in abundance of key mRNA transcripts encoding nine gene products associated with reproduction, stress, metal toxicity, and exposure to environmental contaminants. Gene expression profiles were characterized in liver and muscle tissue of pre- and post-migration Sockeye and Chinook salmon. The results of stock-matched animals indicate that dynamic changes in mRNA levels occur for a number of genes in both species during migration and suggest that Sockeye salmon exhibit a greater level of biological stress compared to the Chinook salmon population. Using a male-specific genotypic marker, we found that out of the 154 animals examined, one Sockeye was genotypically male but phenotypically female. This individual's gene expression profile in liver and muscle was reminiscent of, but not identical to, the female expression profile. These studies provide the first glimpse of the dynamic yet common nature of changes in the transcriptome that are shared between species during in-migration and highlight differences that may relate to population success. Continued longitudinal assessment will further define the association between contaminant burden, physiological stress, and modulation of gene expression in migrating Pacific salmon.

Swimming suppresses hepatic vitellogenesis in European female silver eels as shown by expression of the estrogen receptor 1, vitellogenin1 and vitellogenin2 in the liver

BACKGROUND

When European silver eels (Anguilla anguilla) venture into the Atlantic Ocean for their 6,000 km semelparous spawning run to the Sargasso Sea, they are still in a prepubertal stage. Further sexual development appears to be blocked by dopaminergic inhibition of hypothalamus and pituitary activity. Recently, we found that swimming for several weeks in freshwater stimulated the incorporation of fat droplets in the oocytes. So, it was hypothesized that long term swimming in seawater would release the inhibition further and would also stimulate the production of vitellogenin by the liver.

METHODS

For this study a swim-flume was constructed to allow simulated migration of migratory female silver eels for 3 months (1,420 km) in natural seawater at 20 degrees C. Primers were designed for polymerase chain reactions to measure the mRNA expression of estrogen receptor 1 (esr1), vitellogenin1 (vtg1) and vitellogenin2 (vtg2) genes in the liver of European female silver eels.

RESULTS

In comparison to resting eels, swimming eels showed a diminished expression of esr1, vtg1 and vtg2 in the liver. They also had lower plasma calcium (Ca; indicative of vitellogenin) levels in their blood. This showed that vitellogenesis is more strongly suppressed in swimming than in resting eels. However, when eels were subsequently stimulated by 3 weekly carp pituitary extract injections, the expression of the same genes and plasma levels of Ca strongly increased in both groups to similar levels, thus equalizing the initial differences between resting and swimming.

CONCLUSIONS

It is concluded that vitellogenesis remains suppressed during resting and even more during swimming. The fact that swimming stimulates fat deposition in the oocytes but suppresses vitellogenesis indicates that these events are separated in nature and occur sequentially. Swimming-suppressed vitellogenesis may imply that in nature eels undergo vitellogenesis and final maturation near or at the spawning grounds.

Proteomic signature of muscle atrophy in rainbow trout

Muscle deterioration arises as a physiological response to elevated energetic demands of fish during sexual maturation and spawning. Previously, we used this model to characterize the transcriptomic mechanisms associated with fish muscle degradation and identified potential biological markers of muscle growth and quality. However, transcriptional measurements do not necessarily reflect changes in active mature proteins. Here we report the characterization of proteomic profile in degenerating muscle of rainbow trout in relation to the female reproductive cycle using a LC/MS-based label-free protein quantification method. A total of 146 significantly changed proteins in atrophying muscles (FDR <5%) was identified. Proteins were clustered according to their gene ontology identifiers. Muscle atrophy was associated with decreased abundance in proteins of anaerobic respiration, protein biosynthesis, monooxygenases, follistatins, and myogenin, as well as growth hormone, interleukin-1 and estrogen receptors. In contrast, proteins of MAPK/ERK kinase, glutamine synthetase, transcription factors, Stat3, JunB, Id2, and NFkappaB inhibitor, were greater in atrophying muscle. These changes are discussed in light of the mammalian muscle atrophy paradigm and proposed fish-specific mechanisms of muscle degradation. These data will help identify genes associated with muscle degeneration and superior flesh quality in rainbow trout, facilitating identification of genetic markers for muscle growth and quality.

Effect of starvation on transcriptomes of brain and liver in adult female zebrafish (Danio rerio)

We used microarray and quantitative real-time PCR (qRT-PCR) analyses in adult female zebrafish (Danio rerio) to identify metabolic pathways regulated by starvation in the liver and brain. The transcriptome of whole zebrafish brain showed little response to 21 days of starvation. Only agouti-related protein 1 (agrp1) significantly responded, with increased expression in brains of starved fish. In contrast, a 21-day period of starvation significantly downregulated 466 and upregulated 108 transcripts in the liver, indicating an overall decrease in metabolic activity, reduced lipid metabolism, protein biosynthesis, proteolysis, and cellular respiration, and increased gluconeogenesis. Starvation also regulated expression of many components of the unfolded protein response, the first such report in a species other than yeast (Saccharomyces cerevisiae) and mice (Mus musculus). The response of the zebrafish hepatic transcriptome to starvation was strikingly similar to that of rainbow trout (Oncorhynchus mykiss) and less similar to mouse, while the response of common carp (Cyprinus carpio) differed considerably from the other three species.

Effect of starvation on global gene expression and proteolysis in rainbow trout (Oncorhynchus mykiss)

Background

Fast, efficiently growing animals have increased protein synthesis and/or reduced protein degradation relative to slow, inefficiently growing animals. Consequently, minimizing the energetic cost of protein turnover is a strategic goal for enhancing animal growth. Characterization of gene expression profiles associated with protein turnover would allow us to identify genes that could potentially be used as molecular biomarkers to select for germplasm with improved protein accretion.

Results

We evaluated changes in hepatic global gene expression in response to 3-week starvation in rainbow trout (Oncorhynchus mykiss). Microarray analysis revealed a coordinated, down-regulated expression of protein biosynthesis genes in starved fish. In addition, the expression of genes involved in lipid metabolism/transport, aerobic respiration, blood functions and immune response were decreased in response to starvation. However, the microarray approach did not show a significant increase of gene expression in protein catabolic pathways. Further studies, using real-time PCR and enzyme activity assays, were performed to investigate the expression of genes involved in the major proteolytic pathways including calpains, the multi-catalytic proteasome and cathepsins. Starvation reduced mRNA expression of the calpain inhibitor, calpastatin long isoform (CAST-L), with a subsequent increase in the calpain catalytic activity. In addition, starvation caused a slight but significant increase in 20S proteasome activity without affecting mRNA levels of the proteasome genes. Neither the mRNA levels nor the activities of cathepsin D and L were affected by starvation.

Conclusion

These results suggest a significant role of calpain and 20S proteasome pathways in protein mobilization as a source of energy during fasting and a potential association of the CAST-L gene with fish protein accretion.

Microarray gene expression analysis in atrophying rainbow trout muscle: a unique nonmammalian muscle degradation model

Muscle atrophy is a physiological response to diverse physiological and pathological conditions that trigger muscle deterioration through specific cellular mechanisms. Despite different signals, the biochemical changes in atrophying muscle share many common cascades. Muscle deterioration as a physiological response to the energetic demands of fish vitellogenesis represents a unique model for studying the mechanisms of muscle degradation in non-mammalian animals. A salmonid microarray, containing 16,006 cDNAs, was used to study the transcriptome response to atrophy of fast-switch muscles from gravid rainbow trout compared with sterile fish. Eighty-two unique transcripts were upregulated and 120 transcripts were downregulated in atrophying muscles. Transcripts having gene ontology identifiers were grouped according to their functions. Muscle deterioration was associated with elevated expression of genes involved in the catheptic and collagenase proteolytic pathways; the aerobic production, buffering, and utilization of ATP; and growth arrest; whereas atrophying muscle showed downregulation of genes encoding a serine proteinase inhibitor, enzymes of anaerobic respiration, muscle proteins as well as genes required for RNA and protein biosynthesis/processing. Therefore, gene transcription of the trout muscle atrophy changed in a manner similar to mammalian muscle atrophy. These changes result in an arrest of normal cell growth, protein degradation, and decreased glycolytic cellular respiration that is characteristic of the fast-switch muscle. For the first time, other changes/mechanisms unique to fish were discussed including genes associated with muscle atrophy.