Transcriptome analysis identifies potential molecular mechanisms for growth of fast muscle in Chinese perch juvenile

Chinese perch (Siniperca chuatsi) is an important commercial fish species in China. Understanding the molecular mechanisms of growth and development of skeletal muscle is helpful for selection breeding and improving the growth rate of Chinese perch. We analyzed histological and transcriptomic differences in fast muscle of Chinese perch between 30 days post hatching (dph) and 60 dph using histological sections and high-throughput RNA-Seq. The results showed that the diameter of muscle fibers in 30 dph Chinese perch was mainly distributed in range of 30 - 40 μm, and that of 60 dph was primarily in the range of 40 - 50 μm. 34 differentially expressed genes (DEGs) were identified in the fast muscle of Chinese perch between 30 and 60 dph, of which 9 were up-regulated and 25 were down-regulated (60 dph vs 30 dph). The DEGs, including MYH4, ENO3, Bag3, krt13 and krt18, are associated with muscle cell differentiation and fusion in Chinese perch. The analysis of the protein-protein interaction network of DEGs revealed that FOS, junb and EGR1 may involve in the development of fast muscle. KEGG enrichment results showed that the up-regulated genes in the 60 dph were associated with several pathways related to metabolism and protein synthesis, such as glycosphingolipid biosynthesis and aminoacyl-tRNA biosynthesis. The results suggest that the development of fast muscle in Chinese perch from 30 to 60 dph is accompanied by an increase in muscle fiber diameter and changes in gene expression related to muscle cell differentiation and protein synthesis. Abbreviations: DEGs, differentially expressed genes; dph, days post hatching; FC, fold change; FDR, False Discovery Rate; GO, Gene Ontology; KEGG, Kyoto Encyclopedia of Genes and Genomes; MyHCs, Myosin heavy chains; qRT-PCR, quantitative real-time PCR.

Review: Understanding fish muscle biology in the indeterminate growth species pacu (Piaractus mesopotamicus)

The muscle phenotype of fish is regulated by numerous factors that, although widely explored, still need to be fully understood. In this context, several studies aimed to unravel how internal and external stimuli affect the muscle growth of these vertebrates. The pacu (Piaractus mesopotamicus) is a species of indeterminate muscular growth that quickly reaches high body weight. For this reason, it adds great importance to the productive sector, along with other round fish. In this context, we aimed to compile studies on fish biology and skeletal muscle growth, focusing on studies by our research group that used pacu as an experimental model along with other species. Based on these studies, new muscle phenotype regulators were identified and explored in vivo, in vitro, and in silico studies, which strongly contribute to advances in understanding muscle growth mechanisms with future applications in the productive sector.

Evolutionary Adaptation of Protein Turnover in White Muscle of Stenothermal Antarctic Fish: Elevated Cold Compensation at Reduced Thermal Responsiveness

Protein turnover is highly energy consuming and overall relates to an organism's growth performance varying largely between species, e.g., due to pre-adaptation to environmental characteristics such as temperature. Here, we determined protein synthesis rates and capacity of protein degradation in white muscle of the cold stenothermal Antarctic eelpout (Pachycara brachycephalum) and its closely related temperate counterpart, the eurythermal common eelpout (Zoarces viviparus). Both species were exposed to acute warming (P. brachycephalum, 0 °C + 2 °C day-1; Z. viviparus, 4 °C + 3 °C day-1). The in vivo protein synthesis rate (Ks) was monitored after injection of 13C-phenylalanine, and protein degradation capacity was quantified by measuring the activity of cathepsin D in vitro. Untargeted metabolic profiling by nuclear magnetic resonance (NMR) spectroscopy was used to identify the metabolic processes involved. Independent of temperature, the protein synthesis rate was higher in P. brachycephalum (Ks = 0.38-0.614 % day-1) than in Z. viviparus (Ks= 0.148-0.379% day-1). Whereas protein synthesis remained unaffected by temperature in the Antarctic species, protein synthesis in Z. viviparus increased to near the thermal optimum (16 °C) and tended to fall at higher temperatures. Most strikingly, capacities for protein degradation were about ten times higher in the Antarctic compared to the temperate species. These differences are mirrored in the metabolic profiles, with significantly higher levels of complex and essential amino acids in the free cytosolic pool of the Antarctic congener. Together, the results clearly indicate a highly cold-compensated protein turnover in the Antarctic eelpout compared to its temperate confamilial. Constant versus variable environments are mirrored in rigid versus plastic functional responses of the protein synthesis machinery.

Energetic Implications of Morphological Changes between Fish Larval and Juvenile Stages Using Geometric Morphometrics of Body Shape

The fish body shape is a key factor that influences multiple traits such as swimming, foraging, mating, migrations, and predator avoidance. The present study describes the body morphological changes and the growth trajectories during the transformation from 24 to 54 days post-hatching in the golden grey mullet, Chelon auratus, using geometric morphometric analysis (GMA). The results revealed a decrease in morphological variability (i.e., morphological disparity) with the somatic growth. The main changes affected head size, elongation, and widening of the body. Given that this variability could affect the metabolism, some individuals with different morphologies and in different ontogenetic developmental stages were selected to estimate their potential respiration rate using the Electron Transport System (ETS) analysis. Differences were detected depending on the developmental stage, and being significantly smaller after 54 days post-hatching. Finally, a multivariate linear regression indicated that the specific ETS activity was partially related to the fish length and body shape. Thus, our findings emphasized the relevance of larval morphological variability for understanding the physiological processes that occur during the development.

Seasonal Pattern of the Effect of Slurry Ice during Catching and Transportation on Quality and Shelf Life of Gilthead Sea Bream

The objective of the present study was the evaluation of the effect of slurry ice, as an alternative cooling medium during harvesting and transportation, on the quality parameters (e.g., microbiological stability, sensory attributes, physicochemical changes) and shelf life of fish. The effect of seasonal variability of seawater temperature on fish preservation using the tested cooling media was also investigated. Gilthead sea bream (Sparus aurata) was slaughtered and transported in different mixtures of conventional flake ice and slurry ice for 24 h. Three mixtures of ice were tested as T: slaughtered in flake ice and transported in flake ice (control), TC: slaughtered in slurry ice and transported in flake ice, T50: slaughtered and transported in slurry ice 50%–flake ice 50%. Samples were subsequently stored isothermally at 0 °C for shelf-life evaluation. Three independent experiments were performed at three different periods, i.e., January, April, and September, referring to a sea water temperature range of 13.3–26.8 °C. Higher sea water temperatures at catching led to lower microbial growth rates and proteolytic enzyme activities and longer shelf life of refrigerated whole fish. The partial replacement of conventional flake ice with slurry ice improved the quality and extended the shelf life of fish at 0 °C by 2–7 days. The results of the study support that the use of slurry ice may enable better quality maintenance and significant shelf-life extension of whole gilthead sea bream.

Life in the freezer: protein metabolism in Antarctic fish

Whole-animal, in vivo protein metabolism rates have been reported in temperate and tropical, but not Antarctic fish. Growth in Antarctic species is generally slower than lower latitude species. Protein metabolism data for Antarctic invertebrates show low rates of protein synthesis and unusually high rates of protein degradation. Additionally, in Antarctic fish, increasing evidence suggests a lower frequency of successful folding of nascent proteins and reduced protein stability. This study reports the first whole-animal protein metabolism data for an Antarctic fish. Groups of Antarctic, Harpagifer antarcticus, and temperate, Lipophrys pholis, fish were acclimatized to a range of overlapping water temperatures and food consumption, whole-animal growth and protein metabolism measured. The rates of protein synthesis and growth in Antarctic, but not temperate fish, were relatively insensitive to temperature and were significantly lower in H. antarcticus at 3°C than in L. pholis. Protein degradation was independent of temperature in H. antarcticus and not significantly different to L. pholis at 3°C, while protein synthesis retention efficiency was significantly higher in L. pholis than H. antarcticus at 3°C. These results suggest Antarctic fish degrade a significantly larger proportion of synthesized protein than temperate fish, with fundamental energetic implications for growth at low temperatures.

Lysosomal Function Impacts the Skeletal Muscle Extracellular Matrix

Muscle development and homeostasis are critical for normal muscle function. A key aspect of muscle physiology during development, growth, and homeostasis is modulation of protein turnover, the balance between synthesis and degradation of muscle proteins. Protein degradation depends upon lysosomal pH, generated and maintained by proton pumps. Sphingolipid transporter 1 (spns1), a highly conserved gene encoding a putative late endosome/lysosome carbohydrate/H⁺ symporter, plays a pivotal role in maintaining optimal lysosomal pH and spns1^−/− mutants undergo premature senescence. However, the impact of dysregulated lysosomal pH on muscle development and homeostasis is not well understood. We found that muscle development proceeds normally in spns1^−/− mutants prior to the onset of muscle degeneration. Dysregulation of the extracellular matrix (ECM) at the myotendinous junction (MTJ) coincided with the onset of muscle degeneration in spns1^−/− mutants. Expression of the ECM proteins laminin 111 and MMP-9 was upregulated. Upregulation of laminin 111 mitigated the severity of muscle degeneration, as inhibition of adhesion to laminin 111 exacerbated muscle degeneration in spns1^−/− mutants. MMP-9 upregulation was induced by tnfsf12 signaling, but abrogation of MMP-9 did not impact muscle degeneration in spns1^−/− mutants. Taken together, these data indicate that dysregulated lysosomal pH impacts expression of ECM proteins at the myotendinous junction.

A higher mitochondrial content is associated with greater oxidative damage, oxidative defenses, protein synthesis and ATP turnover in resting skeletal muscle

An unavoidable consequence of aerobic metabolism is the production of reactive oxygen species (ROS). Mitochondria have historically been considered the primary source of ROS; however, recent literature has highlighted the uncertainty in primary ROS production sites and it is unclear how variation in mitochondrial density influences ROS-induced damage and protein turnover. Fish skeletal muscle is composed of distinct, highly aerobic red muscle and anaerobic white muscle, offering an excellent model system in which to evaluate the relationship of tissue aerobic capacity and ROS-induced damage under baseline conditions. The present study used a suite of indices to better understand potential consequences of aerobic tissue capacity in red and white muscle of the pinfish, Lagodon rhomboides. Red muscle had a 7-fold greater mitochondrial volume density than white muscle, and more oxidative damage despite also having higher activity of the antioxidant enzymes superoxide dismutase and catalase. The dominant protein degradation system appears to be tissue dependent. Lysosomal degradation markers and autophagosome volume density were greater in white muscle, while ubiquitin expression and 20S proteasome activity were significantly greater in red muscle. However, ubiquitin ligase expression was significantly higher in white muscle. Red muscle had a more than 2-fold greater rate of translation and total ATP turnover than white muscle, results that may be due in part to the higher mitochondrial density and the associated increase in oxidative damage. Together, these results support the concept that an elevated aerobic capacity is associated with greater oxidative damage and higher costs of protein turnover.

A Multi-Biomarker Approach in European Sea Bass Exposed to Dynamic Temperature Changes under Dietary Supplementation with Origanum vulgare Essential Oil

A feeding trial for 150 days was carried out to evaluate the cross-effects between oregano essential oil (EO) dietary supplementation and dynamic temperature change in sea bass. Under exposure to rising temperature (13-25 °C), fish were fed with a control diet (CD) and two experimental diets supplemented with 100 (D100) and 200 ppm (D200) of EO. Feed inclusion of EO promoted the activity of antioxidant enzymes in sea bass exposed to increasing temperature. Consistently with the temperature rise, TBARS concentrations increased in CD and D200 groups, whereas were almost stable in D100. Trend of blood glucose in fish fed on CD was likely affected by glycogenolysis and gluconeogenesis. Similarly, the depletion of triglycerides and cholesterol in fish fed on CD likely supported the energy cost of gluconeogenesis. On the other hand, the reduction of glucose, triglycerides, and cholesterol in D100 and D200 was mainly attributable to the hypoglycemic and hypolipidemic effects of EO. The higher levels of serum protein observed in D100 and D200 groups were also associated to a reduced thermal stress compared to CD. EO dietary supplementation may be a promising strategy to alleviate the negative effects of temperature shift on sea bass physiological and oxidative state.

What metabolic, osmotic and molecular stress responses tell us about extreme ambient heatwave impacts in fish at low salinities: The case of European seabass, Dicentrarchus labrax

Unprecedented shifts in temperature and precipitation patterns in recent decades place multiple abiotic stressors on the fish. In teleosts, metabolic, osmoregulatory, and molecular potential as tolerance responses to extreme ambient heatwave events at different salinities are poorly understood. The study was performed to evaluate the physio-biochemical stress responses and acclimation potential of European seabass, Dicentrarchus labrax maintained at four different salinities followed by an extreme ambient heatwave exposure. Fish were kept at 32, 12, 6, and 2 psu for 35 days followed by a simulated extreme ambient heatwave (33 °C) exposure for 10 days. Fish growth performances, physio-biochemical and molecular responses were recorded. Fish acclimated at 32 and 2 psu exhibited significantly (p < 0.05) decreased growth performance. Serum [Na⁺] and [Cl^-] ions were significantly lowered (p < 0.05) in 32 psu fish on day 10 of heatwave exposure. While serum glucose, triglycerides, and protein tended to decrease during the extreme ambient heatwave exposure, lactate content increased significantly (p < 0.05) in 32 psu fish on day 10. In 32 and 2 psu fish, serum metabolic enzymes, and cortisol levels increased significantly (p < 0.05) during the extreme heatwave exposure. On days 5 and 10, HSP70 mRNA was significantly (p < 0.05) upregulated in kidneys and gills of 32 and 2 psu fish, while Igf1 showed downregulation. In gills of 2 psu fish, ATPase Na⁺/K⁺-α1 and NKCC1 expression decreased significantly (p < 0.05) in 2 psu, in contrast, significant upregulation was observed at 32 psu fish during extreme ambient heatwave exposure. On days 5 and 10, cystic fibrosis transmembrane conductance (CFTR) upregulation was significantly lower (p < 0.05) in 32 and 2 psu fish. Results suggest that European seabass held at 12 and 6 psu water fare better physiological fitness during the tested extreme ambient heatwave event (33 °C), providing possible insights into options for future aquaculture management in a warming environment.

Effects of crowding on the three main proteolytic mechanisms of skeletal muscle in rainbow trout (Oncorhynchus mykiss)

Background

Skeletal muscle is one of the tissues most affected by stress conditions. The protein degradation in this tissue is vital for the supply of energy mediated by different proteolytic pathways such as the ubiquitin-proteasome (UPS), autophagy-lysosome (ALS) and the calpain/calpastatin system (CCS). Nevertheless, the regulation of this proteolytic axis under stress conditions is not yet completely clear. Chile is the main producer of rainbow trout (Oncorhynchus mykiss) in the world. This intensive fish farming has resulted in growing problems as crowding and stress are one of the major problems in the freshwater stage. In this context, we evaluated the crowding effect in juvenile rainbow trout kept in high stocking density (30 kg/m³) for 15, 45 and 60 days, using a control group of fish (10 kg/m³).

Results

Plasmatic cortisol and glucose were evaluated by enzyme immunoassay. The mRNA levels of stress-related genes (gr1, gr2, mr, hsp70, klf15 and redd1), markers of the UPS (atrogin1 and murf1) and CCS (capn1, capn1, cast-l and cast-s) were evaluated using qPCR. ALS (LC3-I/II and P62/SQSTM1) and growth markers (4E-BP1 and ERK) were measured by Western blot analysis. The cortisol levels increased concomitantly with weight loss at 45 days of crowding. The UPS alone was upregulated at 15 days of high stocking density, while ALS activation was observed at 60 days. However, the CCS was inactivated during the entire trial.

Conclusion

All these data suggest that stress conditions, such as crowding, promote muscle degradation in a time-dependent manner through the upregulation of the UPS at early stages of chronic stress and activation of the ALS in long-term stress, while the CCS is strongly inhibited by stress conditions in the rainbow trout muscle farmed during freshwater stage. Our descriptive study will allow perform functional analysis to determine, in a more detailed way, the effect of stress on skeletal muscle physiology as well as in the animal welfare in rainbow trout. Moreover, it is the first step to elucidate the optimal crop density in the freshwater stage and improve the standards of Chilean aquaculture.

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.

Proteomic Strategies to Evaluate the Impact of Farming Conditions on Food Quality and Safety in Aquaculture Products

This review presents the primary applications of various proteomic strategies to evaluate the impact of farming conditions on food quality and safety in aquaculture products. Aquaculture is a quickly growing sector that represents 47% of total fish production. Food quality, dietary management, fish welfare, the stress response, food safety, and antibiotic resistance, which are covered by this review, are among the primary topics in which proteomic techniques and strategies are being successfully applied. The review concludes by outlining future directions and potential perspectives.

Effects of fasting and refeeding on protein and glucose metabolism in Arctic charr

Refeeding, following a period of food deprivation will often lead to compensatory growth. Although many studies have focused on molecular mechanisms behind this accelerated growth response in fish, little is known on the roles of protein and metabolism. We also assessed, for the first time, the potential roles of miRNAs in regulating compensatory growth. Artcic charr, Salvelinus alpinus, a northern freshwater species, was deprived of food for 101 days and then fed to satiety for 126 days. The refeeding period resulted in compensatory growth, with a partial compensation of body mass. The feed deprivation period lead to a decrease in hepatosomatic index (HSI) and intestinal somatic index (ISI). HSI and ISI were then gradually replenished during early refeeding, following a lag phase prior to the compensatory growth response. mRNA transcripts regulating protein degradation via the autophagy pathway (Cathepsin D and Cathepsin L) in muscle were upregulated during feed restriction and downregulated after refeeding, which could allow for greater protein accretion in muscle, facilitating compensatory growth. Transcript levels from the ubiquitin proteasome pathway (Mafbx and Murf1) and the calpain system (Calpain 7 and Calpastatin) suggested that these pathways were not involved in regulating compensatory growth. Furthermore, we've shown that miRNAs (miR-29a and miR-223) could be involved in fish glycogen homeostasis during the early stages of refeeding. These findings provide a deeper understanding of the molecular mechanisms regulating growth in fish.

Protein degradation systems in the skeletal muscles of parr and smolt Atlantic salmon Salmo salar L. and brown trout Salmo trutta L

Although protein degradation limits the rate of muscle growth in fish, the role of proteolytic systems responsible for degrading myofibrillar proteins in skeletal muscle is not well defined. The study herein aims to evaluate the role of calpains (calcium-activated proteases) and proteasomes (ATP-dependent proteases) in mediating muscle protein turnover at different life stages in wild salmonids. Protease activities were estimated in Atlantic salmon (Salmo salar L.) and brown trout (Salmo trutta L.) parr and smolts from the Indera River (Kola Peninsula, Russia). Calpain and proteasome activities in Atlantic salmon skeletal muscles were lower in smolts as compared with parr. Reduced muscle protein degradation accompanying Atlantic salmon parr-smolt transformation appeared to provide intense muscle growth essential for a minimum threshold size achievement that is required for smoltification. Calpain and proteasome activities in brown trout parr and smolts at age 3+ did not significantly differ. However, calpain activity was higher in smolts brown trout 4+ as compared with parr, while proteasome activity was lower. Results suggest that brown trout smoltification does not correspond with intense muscle growth and is more facultative and plastic in comparison with Atlantic salmon smoltification. Obtained data on muscle protein degradation capacity as well as length-weight parameters of fish reflect differences between salmon and trout in growth and smoltification strategies.