Proteomic signature of muscle atrophy in rainbow trout

Maternal dietary choline levels cause transcriptome shift due to genotype-by-diet interactions in rainbow trout (Oncorhynchus mykiss)

The objective of this study was to identify metabolic regulatory mechanisms affected by choline availability in rainbow trout (Oncorhynchus mykiss) broodstock diets associated with increased offspring growth performance. Three customized diets were formulated to have different levels of choline: (a) 0 % choline supplementation (Low Choline: 2065 ppm choline), (b) 0.6 % choline supplementation (Medium Choline: 5657 ppm choline), and (c) 1.2 % choline supplementation (High Choline: 9248 ppm choline). Six all-female rainbow trout families were fed experimental diets beginning 18 months post-hatch until spawning at 22 months post-hatch; their offspring were fed a commercial diet. Experimental broodstock diet did not affect overall choline, fatty acid, or amino acid content in the oocytes (p > 0.05), apart from tyrosine (p ≤ 0.05). Offspring body weights from the High and Low Choline diets did not differ from those in the Medium Choline diet (p > 0.05); however, family-by-diet and sire-by-diet interactions on offspring growth were detected (p ≤ 0.05). The High Choline diet did not improve growth performance in the six broodstock families at final harvest (520-days post-hatch, or dph). Numerous genes associated with muscle development and lipid metabolism were identified as affected by broodstock diet, including myosin, troponin C, and fatty acid binding proteins, which were associated with key signaling pathways of lipid metabolism, muscle cell development, muscle cell proliferation, and muscle cell differentiation. These findings indicate that supplementing broodstock diets with choline does regulate expression of genes related to growth and nutrient partitioning but does not lead to growth benefits in rainbow trout families selected for disease resistance.

Maternal Transfer and Effects of Selenium on Early Life Stage Development of Redside Shiner (Richardsonius balteatus)

Maternal transfer of selenium (Se) to developing fish eggs during vitellogenesis can cause larval deformity and mortality. Previous studies have shown wide variation among fish species in both the magnitude of maternal transfer (exposure) and the egg Se concentration causing effects (sensitivity). We studied maternal transfer and effects of Se on early life stage development, survival, and growth of redside shiner (Richardsonius balteatus), a small-bodied cyprinid that has been reported to have relatively high ovary:muscle Se concentration ratios. Gametes were collected from lentic areas in southeast British Columbia (Canada) with a range of dietary Se concentrations related to weathering of waste rock from coal mining. Eggs were fertilized and reared in the laboratory from hatch to the onset of exogenous feeding. Larvae were assessed for survival, length, weight, Se-characteristic deformities, and edema. Eggs from a total of 56 females were collected, with egg Se concentrations from 0.7 to 28 mg/kg dry weight. Maternal transfer varied among sites, with egg:muscle Se concentration ratios ranging from <1 to >4. We also found that sampling residual ovaries can overestimate Se concentrations in ripe eggs by up to a factor of 5.7. A correlation between larval weight and egg Se concentration was identified, although the relationship was weak (r2  < 0.1) and appeared to be a site effect. No other relationships were observed between larval endpoints and egg Se concentrations up to the highest concentration tested, indicating that the effects threshold for this species may be >28 mg/kg dry weight in eggs. These data indicate that redside shiner is less sensitive to maternally transferred Se than most other tested fish species. Environ Toxicol Chem 2023;42:2350-2357. © 2023 SETAC.

Transcriptomic insight into the hybridization mechanism of the Tambacu, a hybrid from Colossoma macropomum (Tambaqui) and Piaractus mesopotamicus (Pacu)

Interspecific hybrids are highly complex organisms, especially considering aspects related to the organization of genetic material. The diversity of possibilities created by the genetic combination between different species makes it difficult to establish a large-scale analysis methodology. An example of this complexity is Tambacu, an interspecific hybrid of Colossoma macropomum (Tambaqui) and Piaractus mesopotamicus (Pacu). Either genotype represents an essential role in South American aquaculture. However, despite this importance, the genetic information for these genotypes is still highly scarce in specialized databases. Using RNA-Seq analysis, we characterized the transcriptome of white muscle from Pacu, Tambaqui, and their interspecific hybrid (Tambacu). The sequencing process allowed us to obtain a significant number of reads (approximately 53 billion short reads). A total of annotated contigs were 37,285, 96,738, and 158,709 for Pacu, Tambaqui, and Tambacu. After that, we performed a comparative analysis of the transcriptome of the three genotypes, where we evaluated the differential expression (Tambacu vs Pacu = 11,156, and Tambacu vs Tambaqui = 876) profile of the transcript and the degree of similarity between the nucleotide sequences between the genotypes. We assessed the intensity and pattern of expression across genotypes using differential expression information. Clusterization analysis showed a closer relationship between Tambaqui and Tambacu. Furthermore, digital differential expression analysis selected some target genes related to essential cellular processes to evaluate and validate the expression through the RT-qPCR. The RT-qPCR analysis demonstrated significantly (p < 0.05) elevated expression of the mafbx, foxo1a, and rgcc genes in the hybrid compared to the parents. Likewise, we can observe genes significantly more expressed in Pacu (mtco1 and mylpfa) and mtco2 in Tambaqui. Our results showed that the phenotype presented by Tambacu might be associated with changes in the gene expression profile and not necessarily with an increase in gene variability. Thus, the molecular mechanisms underlying these "hybrid effects" may be related to additive and, in some cases, dominant regulatory interactions between parental alleles that act directly on gene regulation in the hybrid transcripts.

Effects of Alternating Electric Field Assisted Freezing-Thawing-Aging Sequence on Data-Independent Acquisition Quantitative Proteomics of Longissimus dorsi Muscle

This study was designed to investigate the differences in the proteomes of bovine Longissimus dorsi (LD) muscle during an alternating electric field (AEF)-assisted freezing-thawing-aging sequence based on a data-independent acquisition strategy. When compared to that of the only postmortem aging (OA) group, the meat quality of the freezing-thawing-aging sequence (FA) and AEF-assisted freezing-thawing-aging sequence (EA) groups showed a declining trend. However, the group assisted by AEF was significantly enhanced in color, water-holding capacity, and tenderness. Three hundred fifty-two proteins in LD muscle were differentially abundant proteins (DAPs) among FA, EA, and OA treatments. Furthermore, among the 40 DAPs in the FA versus EA comparison, 5 DAPs with variable importance in projection scores higher than 1 were identified as biochemical markers of beef quality. Bioinformatic analysis revealed that most of these proteins were involved in structural constituents of ribosome and catalytic activity. These results provide a basis for further understanding the quality of beef following a freezing-thawing-aging sequence assisted by AEF.

Hydroxytyrosol-rich extract from olive juice as an additive in gilthead sea bream juveniles fed a high-fat diet: Regulation of somatic growth

The dietary inclusion of plant-based products in fish feeds formulation is required for the sustainable development of aquaculture. Moreover, considering functional diets, hydroxytyrosol, one of the major phenolic compounds found in olives (Olea europaea), has been identified as a potential candidate to be used in the aquafeeds industry due to its health promoting abilities. The aim of this study was to evaluate the effects of the inclusion of an olive juice extract rich in hydroxytyrosol as an additive (0.52 g HT/kg feed) in a high-fat (24% lipids) diet in gilthead sea bream (Sparus aurata) juveniles. Moreover, the experimental diets, with or without the extract, were administered daily at a standard (3% of total biomass in the tank) or restricted ration (40% reduction) for 8–9 weeks. Growth and biometric parameters, insulin-like growth factor 1 (IGF-1) plasma levels and growth hormone/IGF axis-, myogenic- and osteogenic-related genes expression in liver, white muscle and/or bone were analyzed. Moreover, in vitro cultures of vertebra bone-derived cells from fish fed the diets at a standard ration were performed at weeks 3 and 9 to explore the effects of hydroxytyrosol on osteoblasts development. Although neither body weight or any other biometric parameter were affected by diet composition after 4 or 8 weeks, the addition of the hydroxytyrosol-rich extract to the diet increased IGF-1 plasma levels, regardless of the ration regime, suggesting an anabolic condition. In muscle, the higher mRNA levels of the binding protein igfbp-5b and the myoblast fusion marker dock5 in fish fed with the hydroxytyrosol-rich diet suggested that this compound may have a role in muscle, inducing development and a better muscular condition. Furthermore in bone, increased osteogenic potential while delayed matrix mineralization after addition to the diet of the olive juice extract was supported by the upregulated expression of igf-1 and bmp4 and reduced transcript levels of osteopontin. Overall, this study provides new insights into the beneficial use of hydroxytyrosol as a dietary additive in gilthead sea bream functional diets to improve muscle-skeletal condition and, the aquaculture industry.

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.

Changes of Gene Expression Patterns of Muscle Pathophysiology-Related Transcription Factors During Denervated Muscle Atrophy

Peripheral nerve injury is common, and can lead to skeletal muscle atrophy and dysfunction. However, the underlying molecular mechanisms are not fully understood. The transcription factors have been proved to play a key role in denervated muscle atrophy. In order to systematically analyze transcription factors and obtain more comprehensive information of the molecular regulatory mechanisms in denervated muscle atrophy, a new transcriptome survey focused on transcription factors are warranted. In the current study, we used microarray to identify and analyze differentially expressed genes encoding transcription factors in denervated muscle atrophy in a rat model of sciatic nerve dissection. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were used to explore the biological functions of differentially expressed transcription factors and their target genes related to skeletal muscle pathophysiology. We found that the differentially expressed transcription factors were mainly involved in the immune response. Based on correlation analysis and the expression trends of transcription factors, 18 differentially expressed transcription factors were identified. Stat3, Myod1, Runx1, Atf3, Junb, Runx2, Myf6, Stat5a, Tead4, Klf5, Myog, Mef2a, and Hes6 were upregulated. Ppargc1a, Nr4a1, Lhx2, Ppara, and Rxrg were downregulated. Functional network mapping revealed that these transcription factors are mainly involved in inflammation, development, aging, proteolysis, differentiation, regeneration, autophagy, oxidative stress, atrophy, and ubiquitination. These findings may help understand the regulatory mechanisms of denervated muscle atrophy and provide potential targets for future therapeutic interventions for muscle atrophy following peripheral nerve injury.

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.

Radiographic characterisation of spinal curvature development in farmed New Zealand Chinook salmon Oncorhynchus tshawytscha throughout seawater production

Spinal anomalies are a recognised source of downgrading in finfish aquaculture, but identifying their cause(s) is difficult and often requires extensive knowledge of the underlying pathology. Late-onset spinal curvatures (lordosis, kyphosis, scoliosis) can affect up to 40% of farmed New Zealand Chinook (king) salmon (Oncorhynchus tshawytscha) at harvest, but little is known about their pathogenesis. Curvature development was radiographically documented in two related cohorts of commercially-farmed Chinook salmon throughout seawater production to determine (1) the timing of radiographic onset and relationships between (2) the curvature types, (3) the spinal regions in which they develop and (4) their associations with co-existing vertebral body anomalies (vertebral compression, fusion and vertical shift). Onset of curvature varied between individuals, but initially occurred eight months post-seawater transfer. There were strong associations between the three curvature types and the four recognised spinal regions: lordosis was predominantly observed in regions (R)1 and R3, kyphosis in R2 and R4, manifesting as a distinct pattern of alternating lordosis and kyphosis from head to tail. This was subsequently accompanied by scoliosis, which primarily manifested in spinal regions R2 and R3, where most of the anaerobic musculature is concentrated. Co-existing vertebral body anomalies, of which vertebral compression and vertical shift were most common, appeared to arise either independent of curvature development or as secondary effects. Our results suggest that spinal curvature in farmed New Zealand Chinook salmon constitutes a late-onset, rapidly-developing lordosis-kyphosis-scoliosis (LKS) curvature complex with a possible neuromuscular origin.

Interactions of long-term food ration variation and short-term fasting on insulin-like growth factor-1 (IGF-1) pathways in copper rockfish (Sebastes caurinus)

Variation in food intake affects somatic growth by altering the expression of hormones in the somatotropic endocrine axis including insulin-like growth factor-1 (IGF-1). Here, we examined IGF-1 pathway responses to long- and short-term variation in food availability in copper rockfish (Sebastes caurinus), a nearshore Pacific rockfish important for commercial and recreational fisheries. Juvenile copper rockfish were raised under differing ration amounts (3% or 9% mass feed·g^-1 fish wet mass·day^-1) for 140 d to simulate 'long-term' feeding variation, after which some fish from both rations were fasted for 12 d to generate 'short-term' conditions of food deprivation. Rockfish on the 9% ration treatment grew more quickly than those on the 3% ration and were larger in mass, length, and body condition (k) after 152 d. Fish on the 9% ration had higher blood glucose than those on the 3% ration, with fasting decreasing blood glucose in both ration treatments, indicating that both long-term and short-term feed treatments altered energy status. Plasma IGF-1 was higher in rockfish from the 9% ration than those in the 3% ration and was also higher in fed fish than fasted fish. Additionally, plasma IGF-1 related positively to individual variation in specific growth rate (SGR). The positive association between IGF-1 and SGR showed discordance in fish that had experienced different levels of food and growth over the long-term but not short-term, suggesting that long-term nutritional experience can influence the relationship between IGF-1 and growth in this species. Rockfish on the 3% ration showed a lower relative abundance of gene transcripts encoding igf1 in the liver, but higher hepatic mRNAs for IGF binding proteins igfbp1a and igfbp1b. Fasting similarly decreased the abundance of igf1 mRNAs in the liver of fish reared under both the 9% and 3% rations, while concurrently increasing mRNAs encoding the IGF binding proteins igfbp1a, -1b, and -3a. Hepatic mRNAs for igfbp2b, -5a, and -5b were lower with long-term ration variation (3% ration) and fasting. Fish that experienced long-term reduced rations also had higher mRNA levels for igfbp3a, -3b, and IGF receptors isoforms A (igf1rA) and B (igf1rB) in skeletal muscle, but lower mRNA levels for igf1. Fasting increased muscle mRNA abundance for igfbp3a, igf1rA, and igf1rB, and decreased levels for igfbp2a and igf1. These data show that a positive relationship between circulating IGF-1 and individual growth rate is maintained in copper rockfish even when that growth variation relates to differences in food consumption across varying time scales, but that long- and short-term variation in food quantity can shift basal concentrations of circulating IGF-1 in this species.

Proteomic analysis of the fast-twitch muscle of pacu (Piaractus mesopotamicus) after prolonged fasting and compensatory growth

Protocols that improve growth performance in fish while assuring product quality are important for aquaculture. Fasting followed by refeeding may promote compensatory growth, thus optimizing growth performance. During fasting and refeeding, fast-twitch muscle, which comprises most of fish fillet, undergoes intense plasticity. In this work, we studied the proteome of pacu (Piaractus mesopotamicus) fast-twitch muscle after 30 days of fasting (D30), 30 days of refeeding (D60) and 60 days of refeeding (D90) with two-dimensional electrophoresis, mass spectrometry and bioinformatics. Body mass, growth rate and muscle histology were also assessed. At D30, fish presented muscle catabolism and decreased growth. Proteomic analysis showed that metabolism proteins were the most affected, up and downregulated. Cytoskeleton and amino acid biosynthesis proteins were downregulated, while nuclear and regulatory proteins were upregulated. At D60, fish showed accelerated growth, despite the body mass not completely recovering. Metabolism proteins were still the most affected. Amino acid biosynthesis proteins became upregulated, while cytoskeleton proteins remained downregulated. At D90, the fish presented total compensatory growth. Many metabolic proteins were up or downregulated. Few cytoskeleton proteins remained differentially expressed. Amino acid biosynthesis proteins were mostly upregulated, but less than at D60. Prolonged fasting followed by refeeding also led to the regulation of possible meat quality biomarkers, such as antioxidant enzymes. This fact suggests possible consequences of this protocol on fish meat quality. Our work also enriches our knowledge on proteomic changes during muscle plasticity that occur during fasting and refeeding diet protocols.

Integrated analysis of lncRNA and mRNA expression in rainbow trout families showing variation in muscle growth and fillet quality traits

Muscle yield and quality traits are important for the aquaculture industry and consumers. Genetic selection for these traits is difficult because they are polygenic and result from multifactorial interactions. To study the genetic architecture of these traits, phenotypic characterization of whole body weight (WBW), muscle yield, fat content, shear force and whiteness were measured in ~500 fish representing 98 families from a growth-selected line. RNA-Seq was used to sequence the muscle transcriptome of different families exhibiting divergent phenotypes for each trait. We have identified 240 and 1,280 differentially expressed (DE) protein-coding genes and long noncoding RNAs (lncRNAs), respectively, in fish families exhibiting contrasting phenotypes. Expression of many DE lncRNAs (n = 229) was positively correlated with overlapping, neighboring or distantly located protein-coding genes (n = 1,030), resulting in 3,392 interactions. Three DE antisense lncRNAs were co-expressed with sense genes known to impact muscle quality traits. Forty-four DE lncRNAs had potential sponge functions to miRNAs that affect muscle quality traits. This study (1) defines muscle quality associated protein-coding and noncoding genes and (2) provides insight into non-coding RNAs involvement in regulating growth and fillet quality 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.

Insulin-Like Growth Factor-Binding Proteins of Teleost Fishes

The insulin-like growth factor (Igf) binding protein (Igfbp) family has a broad range of physiological functions and a fascinating evolutionary history. This review focuses on the Igfbps of teleost fishes, where genome duplication events have diversified gene repertoire, function, and physiological regulation-with six core Igfbps expanded into a family of over twenty genes in some lineages. In addition to briefly summarizing the current state of knowledge on teleost Igfbp evolution, function, and expression-level regulation, we highlight gaps in our understanding and promising areas for future work.

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.

Proteomic signature of muscle fibre hyperplasia in response to faba bean intake in grass carp

Fish muscle growth is important for the rapidly developing global aquaculture industry, particularly with respect to production and quality. Changes in muscle fibre size are accomplished by altering the balance between protein synthesis and proteolysis. However, our understanding regarding the effects of different protein sources on fish muscle proteins is still limited. Here we report on the proteomic profile of muscle fibre hyperplasia in grass carp fed only with whole faba bean. From the results, a total of 99 significantly changed proteins after muscle hyperplasia increase were identified (p < 0.05, ratio <0.5 or >2). Protein–protein interaction analysis demonstrated the presence of a network containing 56 differentially expressed proteins, and muscle fibre hyperplasia was closely related to a protein–protein network of 12 muscle component proteins. Muscle fibre hyperplasia was also accompanied by decreased abundance in the fatty acid degradation and calcium signalling pathways. In addition, metabolism via the pentose phosphate pathway decreased in grass carp after ingestion of faba bean, leading to haemolysis. These findings could provide a reference for the prevention and treatment of human glucose-6-phosphate dehydrogenase deficiency (“favism”).

Modifications in the proteome of rainbow trout (Oncorhynchus mykiss) embryo and fry as an effect of triploidy induction

Two-dimensional gel electrophoresis (2-DE), matrix-assisted laser desorption/ionization tandem time-of-flight (MALDI-TOF/TOF) mass spectrometry, and database searching were used to analyze the effects of triploidization heat shock treatment on protein expression in rainbow trout eyed embryo and fry. After fertilization, the eggs were incubated at 10 °C for 10 min. Half of the eggs were then subjected to heat shock for 10 min submerged in a 28 °C water bath to induce triploidy. The remainder was incubated normally and used as diploid controls. Specimens of eyed embryos and fry were taken on 18 and 76 days post-fertilization, respectively. In the eyed embryo extracts, seven protein spots were significantly changed in abundance between the control and heat-shocked groups and one of these was decreased while the others were increased in the heat shock-treated group. Of the spots that were shown to change in abundance in the eyed embryos with heat shock treatment, two were identified as vitellogenin, while the others were creatine kinase and angiotensin I. In the 2-DE from the fry muscle extraction, 23 spots were significantly changed in abundance between the diploid and triploid groups. Nineteen of these showed a decreased abundance in diploids, while the remaining four spots had an increased abundance. Triploidization caused differential expression of muscle metabolic proteins including triosephosphate isomerase, glyceraldehyde-3-phosphate dehydrogenase, and beta-enolase. Myosin heavy chain as a structural protein was also found to change in abundance in triploids. The altered expression of both structural and metabolic proteins in triploids was consistent with their increased cell size and lower growth performance.

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 of the Bordetella pertussis secretome under different media

Our understanding of the Bordetella pertussis secretome remains limited including the role of different growth conditions in the secretome. In this study the secretome of L1423, a clinical isolate from the 2008-2012 Australian epidemic, cultured on Stainer-Scholte (SS) and Thalen-IJssel (THIJS) media for 12h was characterised using liquid chromatography-mass spectrometry (LC-MS/MS). In the supernatant, LC-MS/MS identified 260 proteins with 143 bioinformatically predicted to be secreted. Eighty percent of proteins were identified in both media. Proteins secreted were functionally associated with cell surface (41%), pathogenicity (16%) and transport (17%). The most abundant proteins identified were pathogenic proteins including toxins (PtxA and CyaA), adhesins (TcfA) and type III secretion (T3SS) proteins. There were 46 proteins found uniquely in THIJS including 8 virulence associated proteins. These included T3SS proteins, adhesins (FhaL and FhaS) and a putative toxin (BP1251). Nine proteins were found uniquely in SS and these were metabolic and transport-related proteins. None of the unique proteins detected in SS were known to be virulence associated. This study found that THIJS promotes secretion of virulence factors based on the number of unique virulence proteins found and may be a growth media of choice for the study of B. pertussis virulence and vaccine development.

BIOLOGICAL SIGNIFICANCE

Over the past two decades, the number of B. pertussis notifications has risen despite vaccination. There is a greater need to understand the biology behind B. pertussis infections. The secretome of B. pertussis in two different media was characterised using LC-MS/MS. The results showed that THIJS promotes secretion of importance virulence factors which may be important for the development of vaccines.

Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research

Advancing the production efficiency and profitability of aquaculture is dependent upon the ability to utilize a diverse array of genetic resources. The ultimate goals of aquaculture genomics, genetics and breeding research are to enhance aquaculture production efficiency, sustainability, product quality, and profitability in support of the commercial sector and for the benefit of consumers. In order to achieve these goals, it is important to understand the genomic structure and organization of aquaculture species, and their genomic and phenomic variations, as well as the genetic basis of traits and their interrelationships. In addition, it is also important to understand the mechanisms of regulation and evolutionary conservation at the levels of genome, transcriptome, proteome, epigenome, and systems biology. With genomic information and information between the genomes and phenomes, technologies for marker/causal mutation-assisted selection, genome selection, and genome editing can be developed for applications in aquaculture. A set of genomic tools and resources must be made available including reference genome sequences and their annotations (including coding and non-coding regulatory elements), genome-wide polymorphic markers, efficient genotyping platforms, high-density and high-resolution linkage maps, and transcriptome resources including non-coding transcripts. Genomic and genetic control of important performance and production traits, such as disease resistance, feed conversion efficiency, growth rate, processing yield, behaviour, reproductive characteristics, and tolerance to environmental stressors like low dissolved oxygen, high or low water temperature and salinity, must be understood. QTL need to be identified, validated across strains, lines and populations, and their mechanisms of control understood. Causal gene(s) need to be identified. Genetic and epigenetic regulation of important aquaculture traits need to be determined, and technologies for marker-assisted selection, causal gene/mutation-assisted selection, genome selection, and genome editing using CRISPR and other technologies must be developed, demonstrated with applicability, and application to aquaculture industries.Major progress has been made in aquaculture genomics for dozens of fish and shellfish species including the development of genetic linkage maps, physical maps, microarrays, single nucleotide polymorphism (SNP) arrays, transcriptome databases and various stages of genome reference sequences. This paper provides a general review of the current status, challenges and future research needs of aquaculture genomics, genetics, and breeding, with a focus on major aquaculture species in the United States: catfish, rainbow trout, Atlantic salmon, tilapia, striped bass, oysters, and shrimp. While the overall research priorities and the practical goals are similar across various aquaculture species, the current status in each species should dictate the next priority areas within the species. This paper is an output of the USDA Workshop for Aquaculture Genomics, Genetics, and Breeding held in late March 2016 in Auburn, Alabama, with participants from all parts of the United States.

Effects of tetraploidy induction on rainbow trout (Oncorhynchus mykiss, Walbaum, 1792) proteome at early stages of development

The aim of the present study was to examine the effects of tetraploidy induction on proteome of rainbow trout during the early stages of development. After insemination, the eggs were incubated at 10°C for 350min. Thereafter, half of the eggs were exposed to a heat-shock of 28°C for 10min. The remainder were incubated normally and used as diploid controls. Fertilized egg specimens were selected 390min post-fertilization. Samples corresponding respectively to eyed embryos and fry stages were also taken on days 18 and 76 post-fertilization. Based on two-dimensional electrophoresis, all spots that were found to differ significantly in abundance between the untreated and heat-shock treated groups were selected for identification using MALDI-TOF/TOF mass spectrometry. Out of 19 protein spots showing altered abundance in the present study, 13 spots were successfully identified. Of the spots that were shown to change in abundance in the fertilized eggs with heat-shock treatment, three were identified as vitellogenin (spots 1, 2 and 3); while the others were creatine kinase (spot 5) and nucleoside diphosphate kinase (spot 6). All of the proteins identified in the embryos were related to vitellogenin (spots 8, 12 and 13). Among the identified spots from the fry muscle extracts, two were identified as beta-globin (spots 14 and 17); while the others were parvalbumin (spots 15 and 16) and creatine kinase (spot 19). The results obtained in our study may now set the ground for investigations on gene regulation and proteome modifications in polyploid fish.

iTRAQ-based quantitative proteomic analysis of longissimus muscle from growing pigs with dietary supplementation of non-starch polysaccharide enzymes

Non-starch polysaccharide enzymes (NSPEs) have long been used in the feed production of monogastric animals to degrade non-starch polysaccharide to oligosaccharides and promote growth performance. However, few studies have been conducted on the effect of such enzymes on skeletal muscle in monogastric animals. To elucidate the mechanism of the effect of NSPEs on skeletal muscle, an isobaric tag for relative and absolute quantification (iTRAQ) for differential proteomic quantitation was applied to investigate alterations in the proteome in the longissimus muscle (LM) of growing pigs after a 50-d period of supplementation with 0.6% NSPEs in the diet. A total of 51 proteins were found to be differentially expressed in the LM between a control group and the NSPE group. Functional analysis of the differentially expressed protein species showed an increased abundance of proteins related to energy production, protein synthesis, muscular differentiation, immunity, oxidation resistance and detoxification, and a decreased abundance of proteins related to inflammation in the LM of the pigs fed NSPEs. These findings have important implications for understanding the mechanisms whereby dietary supplementation with NSPEs enzymes can promote growth performance and improve muscular metabolism in growing pigs.

A quantitative proteomic analysis of cellular responses to high glucose media in Chinese hamster ovary cells

A goal in recombinant protein production using Chinese hamster ovary (CHO) cells is to achieve both high specific productivity and high cell density. Addition of glucose to the culture media is necessary to maintain both cell growth and viability. We varied the glucose concentration in the media from 5 to 16 g/L and found that although specific productivity of CHO-DG44 cells increased with the glucose level, the integrated viable cell density decreased. To examine the biological basis of these results, we conducted a discovery proteomic study of CHO-DG44 cells grown under batch conditions in normal (5 g/L) or high (15 g/L) glucose over 3, 6, and 9 days. Approximately 5,000 proteins were confidently identified against an mRNA-based CHO-DG44 specific proteome database, with 2,800 proteins quantified with at least two peptides. A self-organizing map algorithm was used to deconvolute temporal expression profiles of quantitated proteins. Functional analysis of altered proteins suggested that differences in growth between the two glucose levels resulted from changes in crosstalk between glucose metabolism, recombinant protein expression, and cell death, providing an overall picture of the responses to high glucose environment. The high glucose environment may enhance recombinant dihydrofolate reductase in CHO cells by up-regulating NCK1 and down-regulating PRKRA, and may lower integrated viable cell density by activating mitochondrial- and endoplasmic reticulum-mediated cell death pathways by up-regulating HtrA2 and calpains. These proteins are suggested as potential targets for bioengineering to enhance recombinant protein production.

Plasma profiling reveals three proteins associated to amyotrophic lateral sclerosis

Objective

Amyotrophic lateral sclerosis (ALS) is the most common adult motor neuron disease leading to muscular paralysis and death within 3–5 years from onset. Currently, there are no reliable and sensitive markers able to substantially shorten the diagnosis delay. The objective of the study was to analyze a large number of proteins in plasma from patients with various clinical phenotypes of ALS in search for novel proteins or protein profiles that could serve as potential indicators of disease.

Methods

Affinity proteomics in the form of antibody suspension bead arrays were applied to profile plasma samples from 367 ALS patients and 101 controls. The plasma protein content was directly labeled and protein profiles obtained using 352 antibodies from the Human Protein Atlas targeting 278 proteins. A focused bead array was then built to further profile eight selected protein targets in all available samples.

Results

Disease-associated significant differences were observed and replicated for profiles from antibodies targeting the proteins: neurofilament medium polypeptide (NEFM), solute carrier family 25 (SLC25A20), and regulator of G-protein signaling 18 (RGS18).

Interpretation

Upon further validation in several independent cohorts with inclusion of a broad range of other neurological disorders as controls, the alterations of these three protein profiles in plasma could potentially provide new molecular markers of disease that contribute to the quest of understanding ALS pathology.

RNA-seq analysis of early hepatic response to handling and confinement stress in rainbow trout

Fish under intensive rearing conditions experience various stressors which have negative impacts on survival, growth, reproduction and fillet quality. Identifying and characterizing the molecular mechanisms underlying stress responses will facilitate the development of strategies that aim to improve animal welfare and aquaculture production efficiency. In this study, we used RNA-seq to identify transcripts which are differentially expressed in the rainbow trout liver in response to handling and confinement stress. These stressors were selected due to their relevance in aquaculture production. Total RNA was extracted from the livers of individual fish in five tanks having eight fish each, including three tanks of fish subjected to a 3 hour handling and confinement stress and two control tanks. Equal amount of total RNA of six individual fish was pooled by tank to create five RNA-seq libraries which were sequenced in one lane of Illumina HiSeq 2000. Three sequencing runs were conducted to obtain a total of 491,570,566 reads which were mapped onto the previously generated stress reference transcriptome to identify 316 differentially expressed transcripts (DETs). Twenty one DETs were selected for qPCR to validate the RNA-seq approach. The fold changes in gene expression identified by RNA-seq and qPCR were highly correlated (R² = 0.88). Several gene ontology terms including transcription factor activity and biological process such as glucose metabolic process were enriched among these DETs. Pathways involved in response to handling and confinement stress were implicated by mapping the DETs to reference pathways in the KEGG database.

Accession Numbers

Raw RNA-seq reads have been submitted to the NCBI Short Read Archive under accession number SRP022881.

Customized Perl Scripts

All customized scripts described in this paper are available from Dr. Guangtu Gao or the corresponding author.

Inflammatory responses in primary muscle cell cultures in Atlantic salmon (Salmo salar)

BACKGROUND

The relationship between fish health and muscle growth is critical for continued expansion of the aquaculture industry. The effect of immune stimulation on the expression of genes related to the energy balance of fish is poorly understood. In mammals immune stimulation results in major transcriptional changes in muscle, potentially to allow a reallocation of amino acids for use in the immune response and energy homeostasis. The aim of this study was to investigate the effects of immune stimulation on fish muscle gene expression.

RESULTS

Atlantic salmon (Salmo salar) primary muscle cell cultures were stimulated with recombinant (r)IL-1β, a major proinflammatory cytokine, for 24 h in order to simulate an acute immune response. The transcriptomic response was determined by RNA hybridization to a 4 × 44 K Agilent Atlantic salmon microarray platform. The rIL-1β stimulation induced the expression of genes related to both the innate and adaptive immune systems. In addition there were highly significant changes in the expression of genes related to regulation of the cell cycle, growth/structural proteins, proteolysis and lipid metabolism. Of interest were a number of IGF binding proteins that were differentially expressed, which may demonstrate cross talk between the growth and immune systems.

CONCLUSION

We show rIL-1β modulates the expression of not only immune related genes, but also that of genes involved in processes related to growth and metabolism. Co-stimulation of muscle cells with both rIGF-I and rIL-1β demonstrates cross talk between these pathways providing potential avenues for further research. This study highlights the potential negative effects of inflammation on muscle protein deposition and growth in fish and extends our understanding of energy allocation in ectothermic animals.

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.

Dietary lysine imbalance affects muscle proteome in zebrafish (Danio rerio): a comparative 2D-DIGE study

Lysine (Lys) is an indispensable amino acid (AA) and generally the first limiting AA in vegetable protein sources in fish feeds. Inadequate dietary Lys availability may limit protein synthesis, accretion and growth of fish. This experiment aimed to further elucidate the role of Lys imbalance on growth by examining the myotomal muscle proteome of juvenile zebrafish (Danio rerio). Quadruplicate groups of 8 fish were fed either a low-Lys [Lys(-), 1.34 g kg(-1)], medium/control (Lys, 2.47 g kg(-1)) or high-Lys [Lys(+), 4.63 g kg(-1)] diet. Fish growth was monitored from 33 to 49 days post-fertilization (dpf) and trunk myotomal muscle proteome of Lys(-) and Lys(+) treatments were screened by 2D-DIGE and MALDI ToF tandem mass spectrometry. Growth rate was negatively affected by diet Lys(-). Out of 527 ± 11 (mean ± S.E.M.) protein spots detected (∼10-150 kDa and 4-7 pI value), 30 were over-expressed and 22 under-expressed in Lys(-) fish (|fold-change| >1.2, p value <0.05). Higher myosin light chains abundance and other myofibrillar proteins in Lys(-) fish pointed to increased sarcomeric degradation, indicating a higher protein turnover for supplying basal energy-saving metabolism rather than growth and muscle protein accretion. The Lys deficiency also possibly induced a higher feeding activity, reflected in the over-expression of beta enolase and mitochondrial ATP synthase. Contrarily, in the faster growing fish [Lys(+)], over-expression of apolipoprotein A-I, F-actin capping protein and Pdlim7 point to increased energy storage as fat and enhanced muscle growth, particularly by mosaic hyperplasia. Thus using an exploratory approach, this study pinpoints interesting candidates for further elucidating the role of dietary Lys on growth of juvenile fish.

Catabolic signaling pathways, atrogenes, and ubiquitinated proteins are regulated by the nutritional status in the muscle of the fine flounder

A description of the intracellular mechanisms that modulate skeletal muscle atrophy in early vertebrates is still lacking. In this context, we used the fine flounder, a unique and intriguing fish model, which exhibits remarkably slow growth due to low production of muscle-derived IGF-I, a key growth factor that has been widely acknowledged to prevent and revert muscle atrophy. Key components of the atrophy system were examined in this species using a detailed time-course of sampling points, including two contrasting nutritional periods. Under basal conditions high amounts of the atrogenes MuRF-1 and Atrogin-1 were observed. During fasting, the activation of the P38/MAPK and Akt/FoxO signaling pathways decreased; whereas, the activation of the IκBα/NFκB pathway increased. These changes in signal transduction activation were concomitant with a strong increase in MuRF-1, Atrogin-1, and protein ubiquitination. During short-term refeeding, the P38/MAPK and Akt/FoxO signaling pathways were strongly activated, whereas the activation of the IκBα/NFκB pathway decreased significantly. The expression of both atrogenes, as well as the ubiquitination of proteins, dropped significantly during the first hour of refeeding, indicating a strong anti-atrophic condition during the onset of refeeding. During long-term refeeding, Akt remained activated at higher than basal levels until the end of refeeding, and Atrogin-1 expression remained significantly lower during this period. This study shows that the components of the atrophy system in skeletal muscle appeared early in the evolution of vertebrates and some mechanisms have been conserved, whereas others have not. These results represent an important achievement for the area of fish muscle physiology, showing an integrative view of the atrophy system in a non-mammalian species and contributing to novel insights on the molecular basis of muscle growth regulation in earlier vertebrates.

RNA-Seq identifies SNP markers for growth traits in rainbow trout

Fast growth is an important and highly desired trait, which affects the profitability of food animal production, with feed costs accounting for the largest proportion of production costs. Traditional phenotype-based selection is typically used to select for growth traits; however, genetic improvement is slow over generations. Single nucleotide polymorphisms (SNPs) explain 90% of the genetic differences between individuals; therefore, they are most suitable for genetic evaluation and strategies that employ molecular genetics for selective breeding. SNPs found within or near a coding sequence are of particular interest because they are more likely to alter the biological function of a protein. We aimed to use SNPs to identify markers and genes associated with genetic variation in growth. RNA-Seq whole-transcriptome analysis of pooled cDNA samples from a population of rainbow trout selected for improved growth versus unselected genetic cohorts (10 fish from 1 full-sib family each) identified SNP markers associated with growth-rate. The allelic imbalances (the ratio between the allele frequencies of the fast growing sample and that of the slow growing sample) were considered at scores >5.0 as an amplification and <0.2 as loss of heterozygosity. A subset of SNPs (n = 54) were validated and evaluated for association with growth traits in 778 individuals of a three-generation parent/offspring panel representing 40 families. Twenty-two SNP markers and one mitochondrial haplotype were significantly associated with growth traits. Polymorphism of 48 of the markers was confirmed in other commercially important aquaculture stocks. Many markers were clustered into genes of metabolic energy production pathways and are suitable candidates for genetic selection. The study demonstrates that RNA-Seq at low sequence coverage of divergent populations is a fast and effective means of identifying SNPs, with allelic imbalances between phenotypes. This technique is suitable for marker development in non-model species lacking complete and well-annotated genome reference sequences.

Seasonal changes in atrophy-associated proteins of the sonic muscle in the big-snout croaker, Johnius macrorhynus (Pisces, Sciaenidae), identified by using a proteomic approach

In most sciaenids, males possess sonic muscles and produce sound through the contraction of these muscles and amplification of the swim bladder. The sonic muscles in some fishes exhibit seasonal changes in size. For example, they are hypertrophic in the spawning season, and atrophic in the non-spawning months. The protein profiles of the sonic muscle, red muscle, and white muscle in the Johnius macrorhynus were shown by two-dimensional electrophoresis (2-DE) and were compared to reveal differential protein expressions. About 80 up-regulated protein spots in the sonic muscle, and 30 spots related to six contractile proteins (fast muscle myosin heavy chain, skeletal alpha actin, alpha actin cardiac, tropomyosin, myosin light chain 2, and myosin light chain 3), four energy metabolic enzymes (enolase, acyl-CoA synthetase, creatine kinase, and cytochrome P450 monooxygenase), and two miscellaneous proteins (DEAD box protein and cyclin H) were identified. Seasonal hypertrophy and atrophy of the sonic muscles related to the reproductive cycle were verified in male big-snout croaker. The contents of some proteins were significantly different in the muscles under these conditions. The levels of cytochrome P450 monooxygenase, fast muscle myosin heavy chain, DEAD box proteins, isocitrate dehydrogenase, and creatine kinase were up-regulated in the hypertrophic muscle, but the levels of alpha actin cardiac, myosin light 2, and myosin light 3 were lower than in the atrophic muscle. Potential reasons for these differences in protein expression related to physiological adaptation are discussed.