Protein growth rate in rainbow trout (Oncorhynchus mykiss) is negatively correlated to liver 20S proteasome activity

Feeding Behavior, Gut Microbiota, and Transcriptome Analysis Reveal Individual Growth Differences in the Sea Urchin Strongylocentrotus intermedius

Growth differentiation among farmed sea urchins (Strongylocentrotus intermedius) poses a significant challenge to aquaculture, with there being a limited understanding of the underlying molecular mechanisms. In this study, sea urchins with varying growth rates, reared under identical conditions, were analyzed for feeding behavior, gut microbiota, and transcriptomes. Large-sized sea urchins demonstrated significantly higher feeding ability and longer duration than smaller ones. The dominant phyla across all size groups were Campylobacterota, Proteobacteria, and Firmicutes, with Campylobacterota showing the highest abundance in small-sized sea urchins (82.6%). However, the families Lachnospiraceae and Pseudomonadaceae were significantly less prevalent in small-sized sea urchins. Transcriptome analysis identified 214, 544, and 732 differentially expressed genes (DEGs) in the large vs. medium, large vs. small, and medium vs. small comparisons, respectively. Gene Ontology and KEGG pathway analyses associated DEGs with key processes such as steroid biosynthesis, protein processing within the endoplasmic reticulum, and nucleotide sugar metabolism. Variations in phagosomes and signaling pathways indicated that size differences are linked to disparities in energy expenditure and stress responses. These findings provide a foundation for future investigations into the regulatory mechanisms underlying growth differences in S. intermedius and provide clues for the screening of molecular markers useful to improve sea urchin production.

Effect of dietary l-glutamine supplementation on the intestinal physiology and growth during Solea senegalensis larval development

The maturation of the intestinal digestive and absorptive functions might limit the amount of absorbed nutrients to fulfil the high requirements of the fast-growing marine fish larva. Glutamine (Gln) has been described to improve intestinal epithelium functions, due to its involvement in energy metabolism and protein synthesis. The purpose of this study was to evaluate dietary 0.2% Gln supplementation on aspects of intestinal physiology, protein metabolism and growth-related genes expression in Senegalese sole larvae. Experiment was carried out between 12 and 33 days post hatching (DPH) and fish were divided into two experimental groups, one fed Artemia spp. (CTRL) and the other fed Artemia spp. supplemented with Gln (GLN). GLN diet had two times more Gln than the CTRL diet. Samples were collected at 15, 19, 26 and 33 DPH for biometry, histology, and digestive enzymes activity, and at 33 DPH for gene expression, protein metabolism and AA content determination. Growth was significantly higher for Senegalese sole fed GLN diet, supported by differences on protein metabolism and growth-related gene expression. Slight differences were observed between treatments regarding the intestinal physiology. Overall, GLN diet seems to be directed to enhance protein metabolism leading to higher larval growth.

Warm acclimation alters antioxidant defences but not metabolic capacities in the Antarctic fish, Notothenia coriiceps

The Southern Ocean surrounding the Western Antarctic Peninsula region is rapidly warming. Survival of members of the dominant suborder of Antarctic fishes, the Notothenioidei, will likely require thermal plasticity and adaptive capacity in key traits delimiting thermal tolerance. Herein, we have assessed the thermal plasticity of several cellular and biochemical pathways, many of which are known to be associated with thermal tolerance in notothenioids, including mitochondrial function, activities of aerobic and anaerobic enzymes, antioxidant defences, protein ubiquitination and degradation in cardiac, oxidative skeletal muscles and gill of Notothenia coriiceps warm acclimated to 4°C for 22 days or 5°C for 42 days. Levels of triacylglycerol (TAG) were measured in liver and oxidative and glycolytic skeletal muscles, and glycogen in liver and glycolytic muscle to assess changes in energy stores. Metabolic pathways displayed minimal thermal plasticity, yet antioxidant defences were lower in heart and oxidative skeletal muscles of warm-acclimated animals compared with animals held at ambient temperature. Despite higher metabolic rates at elevated temperature, energy storage depots of TAG and glycogen increase in liver and remain unchanged in muscle with warm acclimation. Overall, our studies reveal that N. coriiceps displays thermal plasticity in some key traits that may contribute to their survival as the Southern Ocean continues to warm.

Seasonal differences in thermal stress susceptibility of diploid and triploid brook trout, Salvelinus fontinalis (Teleostei, Pisces)

Many physiological processes of teleost fish show periodicity due to intrinsic rhythms. It may be hypothesized that also susceptibility to thermal stress differs seasonally. To shed more light on this problem the following experiment was conducted. Diploid and triploid Salvelinus fontinalis were kept at an acclimation temperature of 9°C and at a natural photoperiod typical for the Northern Hemisphere during their entire live. During eight different periods of the year, different subgroups were exposed to a 32 day lasting thermal stress of 20°C. Rate of fish maintaining equilibrium, daily growth rate, condition factor, viscerosomatic index and hepato-somatic index were measured. Complementary mRNA expression of genes characterizing growth (GHR1, GHR2), proteolysis (Protreg, Protα5), stress (Hsp47, Hsp90) and respiratory energy metabolism (ATPJ52) was determined. Seasonal differences in thermal stress susceptibility of 2n and 3n S. fontinalis were detected. It was highest from September to December and moderate from January to March. During the remaining period of the year, susceptibility to thermal stress was minimal. Increased thermal stress susceptibility was related to decreased rates of fish maintaining equilibrium, decreased growth rates, reduction of viscera and liver mass and changes in mRNA expression of genes characterizing proteolysis, growth, respiratory energy metabolism and stress. The differences in seasonal stress susceptibility were minor between 2n and 3n S. fontinalis. The data are valuable for ecology and fish culture to identify periods when animals are most susceptible to thermal stress.

Protein metabolism in the liver and white muscle is associated with feed efficiency in Chinook salmon (Oncorhynchus tshawytscha) reared in seawater: Evidence from proteomic analysis

Understanding the molecular mechanisms that underlie differences in feed efficiency (FE) is an important step toward optimising growth and achieving sustainable salmonid aquaculture. In this study, the liver and white muscle proteomes of feed efficient (EFF) and inefficient (INEFF) Chinook salmon (Oncorhynchus tshawytscha) reared in seawater were investigated by liquid chromatography-tandem mass spectrometry (LC-MS/MS). In total, 2746 liver and 702 white muscle proteins were quantified and compared between 21 EFF and 22 INEFF fish. GSEA showed that gene sets related to protein synthesis were enriched in the liver and white muscle of the EFF group, while conversely, pathways related to protein degradation (amino acid catabolism and proteolysis, respectively) were the most affected processes in the liver and white muscle of INEFF fish. Estimates of individual daily feed intake and share of the meal within tank were significantly higher in the INEFF than the EFF fish showing INEFF fish were likely more dominant during feeding and overfed. Overeating by the INEFF fish was associated with an increase in protein catabolism. This study found that fish with different FE values had expression differences in the gene sets related to protein turnover, and this result supports the hypothesis that protein metabolism plays a role in FE.

Why Do Some Rainbow Trout Genotypes Grow Better With a Complete Plant-Based Diet? Transcriptomic and Physiological Analyses on Three Isogenic Lines

Within the context of a growing aquaculture production coupled with a plateau of the production in the main components of aquafeeds (fish oil and fishmeal), recent studies have typically focused on replacing these feedstuffs with terrestrial plant ingredients for cultured carnivorous aquatic species, such as rainbow trout (Oncorhynchus mykiss). Substitution rates without adverse effects have, however, reached their limit. One potential way forward would be to take advantage of the genetic variability that exists in the salmonid population. However, to date, little is known about the underlying molecular mechanisms responsible for this genetic variability. The aim of the present research was to understand why some genotypes are better able to utilize plant-based diets devoid of marine resources. In this regard, three isogenic lines of rainbow trout (R23h, AB1h, and A22h), with similar growth when fed marine resources-based diets and which differ greatly in their responses to a plant-based diet, were fed with either a complete plant-based diet (V diet) or a marine resources-based diet (M diet) since first-feeding. Fish traits and the hepatic transcriptome of these three genotypes were compared after 5 months of feeding. First, differences in the ability to grow with the V diet observed amongst genotypes was not due to higher feed intake, but instead due to differences in feed efficiency. The comparison of transcriptome profiles revealed 575 (R23h vs. AB1h), 1,770 (R23h vs. A22h), and 2,973 (AB1h vs. A22h) probes differentially expressed amongst the three genotypes when fed the V diet. Interestingly, R23h and AB1h fish, which were the least affected by the V diet, exhibited the highest growth. These results demonstrate that these fish were able to maintain a high level of energy production and protein synthesis. Moreover, these genotypes were also able to activate pathways linked to lipid and cholesterol metabolisms, such as the biosynthesis of long-chain polyunsaturated fatty acids. Finally, as previously, immunity seems to also play an important role in the ability of fish to use the V diet, and further studies are needed to understand the mechanisms by which immunity interacts with growth.

Dietary Antioxidant Supplementation Promotes Growth in Senegalese Sole Postlarvae

Somatic growth is a balance between protein synthesis and degradation, and it is largely influenced by nutritional clues. Antioxidants levels play a key role in protein turnover by reducing the oxidative damage in the skeletal muscle, and hence promoting growth performance in the long-term. In the present study, Senegalese sole postlarvae (45 days after hatching, DAH) were fed with three experimental diets, a control (CTRL) and two supplemented with natural antioxidants: curcumin (CC) and grape seed (GS). Trial spanned for 25 days and growth performance, muscle cellularity and the expression of muscle growth related genes were assessed at the end of the experiment (70 DAH). The diets CC and GS significantly improved growth performance of fish compared to the CTRL diet. This enhanced growth was associated with larger muscle cross sectional area, with fish fed CC being significantly different from those fed the CTRL. Sole fed the CC diet had the highest number of muscle fibers, indicating that this diet promoted muscle hyperplastic growth. Although the mean fiber diameter did not differ significantly amongst treatments, the proportion of large-sized fibers (>25 μm) was also higher in fish fed the CC diet suggesting increased hypertrophic growth. Such differences in the phenotype were associated with a significant up-regulation of the myogenic differentiation 2 (myod2) and the myomaker (mymk) transcripts involved in myocyte differentiation and fusion, respectively, during larval development. The inclusion of grape seed extract (GS diet) resulted in a significant increase in the expression of myostatin1. These results demonstrate that both diets (CC and GS) can positively modulate muscle development and promote growth in sole postlarvae. This effect is more prominent in CC fed fish, where increased hyperplastic and hypertrophic growth of the muscle was associated with an upregulation of myod2 and mymk genes.

The combination of resveratrol and exercise enhances muscle growth characteristics in pacu (Piaractus mesopotamicus)

Pacu is a tropical fish with important value to aquaculture. During cellular metabolism, reactive oxygen species (ROS) are produced, which can influence muscle growth. Resveratrol is an effective antioxidant that scavenges ROS and can modulate physical performance preventing oxidative stress. We investigated the effects of resveratrol and exercise on pacu muscle growth characteristics. Four groups were used: fish fed with control diet /without exercise (C); fish fed with control diet/subjected to exercise (CE); fish fed resveratrol-supplemented diet/without exercise (R); and fish fed resveratrol-supplemented diet/subjected to exercise (RE). At 30 days, the RE group presented a significant increase in body weight, fewer muscle fibers in the 20-40 μm and more fibers in the >60 μm diameter class compared to the C group. At day 7, catalase activity decreased in CE and RE groups. Superoxide dismutase activity decreased only in the CE group. Myod and mtor gene expression was higher in R and RE and igf-1 was up-regulated in the RE group. Murf1a level decreased in CE, R, and RE, while sdha expression was higher in the RE group. We suggest that resveratrol in combination with exercise was beneficial for muscle growth and metabolism, increasing the expression levels of genes related to muscle anabolism and oxidative metabolism, besides the decrease of catabolic gene expression. Notably, all of these changes occurred together with muscle hypertrophy and increased body weight. Our results show a positive application for resveratrol in association with exercise as a strategy to improve the growth performance of juvenile pacus.

Selection for feed efficiency in Atlantic salmon using individual indicator traits based on stable isotope profiling

Background

We used stable isotope profiling (¹⁵N and ¹³C) to obtain indicator phenotypes for feed efficiency in aquaculture. Our objectives were to (1) examine whether atom percent of stable isotopes of nitrogen and carbon can explain more of the variation in feed conversion ratio than growth alone, and (2) estimate the heritabilities of and genetic correlations between feed efficiency, growth and indicator traits as functions of nitrogen and carbon metabolism in various tissues. A 12-day experiment was conducted with 2281 Atlantic salmon parr, with an average initial weight of 21.8 g, from 23 full-sib families that were allocated to 46 family tanks and fed an experimental diet enriched with ¹⁵N and ¹³C.

Results

Using leave-one-out cross-validation, as much as 79% of the between-tank variation in feed conversion ratio was explained by growth, indicator traits, and sampling day, compared to 62% that was explained by growth and sampling day alone. The ratio of tissue metabolism, estimated by a change in isotope fractions relative to body growth, was used as an individual indicator for feed efficiency. For these indicator ratio traits, the estimated genetic correlation to feed conversion ratio approached unity but their heritabilities were low (0.06 to 0.11). These results indicate that feed-efficient fish are characterized by allocating a high fraction of their metabolism to growth. Among the isotope indicator traits, carbon metabolism in the liver had the closest estimated genetic correlation with feed conversion ratio on a tank level (− 0.9) but a low estimated genetic correlation with individually recorded feed efficiency indicator ratio traits. The underlying determinants of these correlations are largely unknown.

Conclusions

Our findings show that the use of indicator ratio traits to assess individual feed efficiency in Atlantic salmon has great prospects in selection programs. Given that large quantities of feeds with contrasting isotope profiles of carbon and/or nitrogen can be produced cost-effectively, the use of stable isotopes to monitor nitrogen and carbon metabolism in various tissues has potential for large-scale recording of individual feed efficiency traits, without requiring individual feed intake to be recorded.

Change in Ubiquitin Proteasome System of Grass Carp Ctenopharyngodon idellus Reared in the Different Stocking Densities

The ubiquitin proteasome system (UPS) is a highly regulated mechanism of intracellular protein degradation and turnover. To evaluate the effect of crowding stress on the UPS in fish, grass carp (Ctenopharyngodon idellus) were randomly reared at low stocking density (LSD, 0.9 kg m⁻²) or high stocking density (HSD, 5.9 kg m⁻²) for 70 days. The expression of the genes regulating UPS, stress-related parameters, and profiles of amino acid in white muscle as well as growth rate of fish reared at two stocking densities were investigated. Fish exhibited significantly higher growth rate in the LSD group compared to the HSD group. Serum concentrations of cortisol, total protein, and glucose did not vary significantly in fish between two groups. There was no significant difference in the mRNA levels of nrf2, keap1, and hsp90 in white muscle of fish stocked at two densities at the endpoint of the experiment. In the UPS pathway, the expressions of ub, chip, psmc1 in the LSD group were significantly higher than those in the HSD group (P < 0.05). Ubiquitinated protein level and the content of 3-Methylhistidine elevated significantly in the LSD group (P < 0.05). The mRNA levels of mafbx, murf1, and s6k1 in the LSD group were significantly higher than those in HSD group (P < 0.05). These results illustrate that the fish cultured in lower stocking density would exhibit a greater growth rate and a fast protein turnover in muscle.

The loss of hemoglobin and myoglobin does not minimize oxidative stress in Antarctic icefishes

The unusual pattern of expression of hemoglobin (Hb) and myoglobin (Mb) among Antarctic notothenioid fishes provides an exceptional model system for assessing the impact of these proteins on oxidative stress. We tested the hypothesis that the lack of oxygen-binding proteins may reduce oxidative stress. Levels and activity of pro-oxidants and small-molecule and enzymatic antioxidants, and levels of oxidized lipids and proteins in the liver, oxidative skeletal muscle and heart ventricle were quantified in five species of notothenioid fishes differing in the expression of Hb and Mb. Levels of ubiquitinated proteins and rates of protein degradation by the 20S proteasome were also quantified. Although levels of oxidized proteins and lipids, ubiquitinated proteins, and antioxidants were higher in red-blooded fishes than in Hb-less icefishes in some tissues, this pattern did not persist across all tissues. Expression of Mb was not associated with oxidative damage in the heart ventricle, whereas the activity of citrate synthase and the contents of heme were positively correlated with oxidative damage in most tissues. Despite some tissue differences in levels of protein carbonyls among species, rates of degradation by the 20S proteasome were not markedly different, suggesting either alternative pathways for eliminating oxidized proteins or that redox tone varies among species. Together, our data indicate that the loss of Hb and Mb does not correspond with a clear pattern of either reduced oxidative defense or oxidative damage.

Molecular pathways associated with the nutritional programming of plant-based diet acceptance in rainbow trout following an early feeding exposure

Background

The achievement of sustainable feeding practices in aquaculture by reducing the reliance on wild-captured fish, via replacement of fish-based feed with plant-based feed, is impeded by the poor growth response seen in fish fed high levels of plant ingredients. Our recent strategy to nutritionally program rainbow trout by early short-term exposure to a plant-based (V) diet versus a control fish-based (M) diet at the first-feeding fry stage when the trout fry start to consume exogenous feed, resulted in remarkable improvements in feed intake, growth and feed utilization when the same fish were challenged with the diet V (V-challenge) at the juvenile stage, several months following initial exposure. We employed microarray expression analysis at the first-feeding and juvenile stages to deduce the mechanisms associated with the nutritional programming of plant-based feed acceptance in trout.

Results

Transcriptomic analysis was performed on rainbow trout whole fry after 3 weeks exposure to either diet V or diet M at the first feeding stage (3-week), and in the whole brain and liver of juvenile trout after a 25 day V-challenge, using a rainbow trout custom oligonucleotide microarray. Overall, 1787 (3-week + Brain) and 924 (3-week + Liver) mRNA probes were affected by the early-feeding exposure. Gene ontology and pathway analysis of the corresponding genes revealed that nutritional programming affects pathways of sensory perception, synaptic transmission, cognitive processes and neuroendocrine peptides in the brain; whereas in the liver, pathways mediating intermediary metabolism, xenobiotic metabolism, proteolysis, and cytoskeletal regulation of cell cycle are affected. These results suggest that the nutritionally programmed enhanced acceptance of a plant-based feed in rainbow trout is driven by probable acquisition of flavour and feed preferences, and reduced sensitivity to changes in hepatic metabolic and stress pathways.

Conclusions

This study outlines the molecular mechanisms in trout brain and liver that accompany the nutritional programming of plant-based diet acceptance in trout, reinforces the notion of the first-feeding stage in oviparous fish as a critical window for nutritional programming, and provides support for utilizing this strategy to achieve improvements in sustainability of feeding practices in aquaculture.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2804-1) contains supplementary material, which is available to authorized users.

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.

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

BACKGROUND

Aquaculture of piscivorous fish is in continual expansion resulting in a global requirement to reduce the dependence on wild caught fish for generation of fishmeal and fish oil. Plant proteins represent a suitable protein alternative to fish meal and are increasingly being used in fish feed. In this study, we examined the transcriptional response of Atlantic salmon (Salmo salar) to a high marine protein (MP) or low fishmeal, higher plant protein replacement diet (PP), formulated to the same nutritional specification within previously determined acceptable maximum levels of individual plant feed materials.

RESULTS

After 77 days of feeding the fish in both groups doubled in weight, however neither growth performance, feed efficiency, condition factor nor organ indices were significantly different. Assessment of histopathological changes in the heart, intestine or liver did not reveal any negative effects of the PP diet. Transcriptomic analysis was performed in mid intestine, liver and skeletal muscle, using an Atlantic salmon oligonucleotide microarray (Salar_2, Agilent 4x44K). The dietary comparison revealed large alteration in gene expression in all the tissues studied between fish on the two diets. Gene ontology analysis showed, in the mid intestine of fish fed PP, higher expression of genes involved in enteritis, protein and energy metabolism, mitochondrial activity/kinases and transport, and a lower expression of genes involved in cell proliferation and apoptosis compared to fish fed MP. The liver of fish fed PP showed a lower expression of immune response genes but a higher expression of cell proliferation and apoptosis processes that may lead to cell reorganization in this tissue. The skeletal muscle of fish fed PP vs MP was characterized by a suppression of processes including immune response, energy and protein metabolism, cell proliferation and apoptosis which may reflect a more energy efficient tissue.

CONCLUSIONS

The PP diet resulted in significant effects on transcription in all the 3 tissues studied. Despite of these alterations, we demonstrated that high level of plant derived proteins in a salmon diet allowed fish to grow with equal efficiency as those on a high marine protein diet, and with no difference in biometric quality parameters.

PROTEOMICS in aquaculture: applications and trends

Over the last forty years global aquaculture presented a growth rate of 6.9% per annum with an amazing production of 52.5 million tonnes in 2008, and a contribution of 43% of aquatic animal food for human consumption. In order to meet the world's health requirements of fish protein, a continuous growth in production is still expected for decades to come. Aquaculture is, though, a very competitive market, and a global awareness regarding the use of scientific knowledge and emerging technologies to obtain a better farmed organism through a sustainable production has enhanced the importance of proteomics in seafood biology research. Proteomics, as a powerful comparative tool, has therefore been increasingly used over the last decade to address different questions in aquaculture, regarding welfare, nutrition, health, quality, and safety. In this paper we will give an overview of these biological questions and the role of proteomics in their investigation, outlining the advantages, disadvantages and future challenges. A brief description of the proteomics technical approaches will be presented. Special focus will be on the latest trends related to the aquaculture production of fish with defined nutritional, health or quality properties for functional foods and the integration of proteomics techniques in addressing this challenging issue.

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.

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

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

Effects of the total replacement of fish-based diet with plant-based diet on the hepatic transcriptome of two European sea bass (Dicentrarchus labrax) half-sibfamilies showing different growth rates with the plant-based diet

Background

Efforts towards utilisation of diets without fish meal (FM) or fish oil (FO) in finfish aquaculture have been being made for more than two decades. Metabolic responses to substitution of fishery products have been shown to impact growth performance and immune system of fish as well as their subsequent nutritional value, particularly in marine fish species, which exhibit low capacity for biosynthesis of long-chain poly-unsaturated fatty acids (LC-PUFA). The main objective of the present study was to analyse the effects of a plant-based diet on the hepatic transcriptome of European sea bass (Dicentrarchus labrax).

Results

We report the first results obtained using a transcriptomic approach on the liver of two half-sibfamilies of the European sea bass that exhibit similar growth rates when fed a fish-based diet (FD), but significantly different growth rates when fed an all-plant diet (VD). Overall gene expression was analysed using oligo DNA microarrays (GPL9663). Statistical analysis identified 582 unique annotated genes differentially expressed between groups of fish fed the two diets, 199 genes regulated by genetic factors, and 72 genes that exhibited diet-family interactions. The expression of several genes involved in the LC-PUFA and cholesterol biosynthetic pathways was found to be up-regulated in fish fed VD, suggesting a stimulation of the lipogenic pathways. No significant diet-family interaction for the regulation of LC-PUFA biosynthesis pathways could be detected by microarray analysis. This result was in agreement with LC-PUFA profiles, which were found to be similar in the flesh of the two half-sibfamilies. In addition, the combination of our transcriptomic data with an analysis of plasmatic immune parameters revealed a stimulation of complement activity associated with an immunodeficiency in the fish fed VD, and different inflammatory status between the two half-sibfamilies. Biological processes related to protein catabolism, amino acid transaminations, RNA splicing and blood coagulation were also found to be regulated by diet, while the expression of genes involved in protein and ATP synthesis differed between the half-sibfamilies.

Conclusions

Overall, the combined gene expression, compositional and biochemical studies demonstrated a large panel of metabolic and physiological effects induced by total substitution of both FM and FO in the diets of European sea bass and revealed physiological characteristics associated with the two half-sibfamilies.

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.

Carbohydrate energy reserves and effects of food deprivation in male and female rainbow trout

We investigated the effects of nutritional state on carbohydrate, lipid, and protein stores in the heart, liver, and white skeletal muscle of male and female rainbow trout. For fed animals we also partitioned glycogen into fractions based on acid solubility. Fish (10-14 months-old, ~400-500 g) were held at 14 °C and either fed (1% of body weight, every other day) or deprived of food for 14 days. Under fed conditions, glycogen was increased 54% in ventricles from males compared with females, and elevated in the liver (87%) and white muscle (70%) in sexually-maturing versus immature males. Acid soluble glycogen predominated over the acid insoluble fraction in all tissues and was similar between sexes. Food deprivation 1) selectively reduced glycogen and free glucose in male ventricles by ~30%, and 2) did not change glycogen in the liver or white muscle, or triglyceride, protein or water levels in any tissues for both sexes. These data highlight sex differences in teleost cardiac stores and the metabolism of carbohydrates, and contrast with mammals where cardiac glycogen increases during fasting and acid insoluble glycogen is a significant fraction. Increased glycogen in the hearts of male rainbow trout appears to pre-empt sex-specific cardiac growth while storage of acid soluble glycogen may reflect a novel strategy for efficient synthesis and mobilization of glycogen in fishes.

White muscle 20S proteasome activity is negatively correlated to growth rate at low temperature in the spotted wolffish Anarhichas minor

The effect of temperature and mass on specific growth rate (G) was examined in spotted wolffish Anarhichas minor of different size classes (ranging from 60 to 1500 g) acclimated at different temperatures (4, 8 and 12 degrees C). The relationship between G and 20S proteasome activity in heart ventricle, liver and white muscle tissue was then assessed in fish acclimated at 4 and 12 degrees C to determine if protein degradation via the proteasome pathway could be imposing a limitation on somatic growth. Cardiac 20S proteasome activity was not affected by acclimation temperature nor fish mass and had no correlation with G. Hepatic 20S proteasome activity was higher at 12 degrees C but did not show any relationship with G. Partial correlation analysis showed that white muscle 20S proteasome activity was negatively correlated to G (partial Pearson's r = -0.609) but only at cold acclimation temperature (4 degrees C). It is suggested that acclimation to cold temperature involves compensation of the mitochondrial oxidative capacity which would in turn lead to increased production of oxidatively damaged proteins that are degraded by the proteasome pathway and ultimately negatively affects G at cold temperature.

Effects of insulin-like growth factor-I, insulin, and leucine on protein turnover and ubiquitin ligase expression in rainbow trout primary myocytes

The effects of insulin-like growth factor-I (IGF-I), insulin, and leucine on protein turnover and pathways that regulate proteolytic gene expression and protein polyubiquitination were investigated in primary cultures of 4-day-old rainbow trout myocytes. Supplementing media with 100 nM IGF-I increased protein synthesis by 13% (P < 0.05) and decreased protein degradation by 14% (P < 0.05). Treatment with 1 microM insulin increased protein synthesis by 13% (P < 0.05) and decreased protein degradation by 17% (P < 0.05). Supplementing media containing 0.6 mM leucine with an additional 2.5 mM leucine did not increase protein synthesis rates but reduced rates of protein degradation by 8% (P < 0.05). IGF-I (1 nM-100 nM) and insulin (1 nM-1 microM) independently reduced the abundance of ubiquitin ligase mRNA in a dose-dependent manner, with maximal reductions of approximately 70% for muscle atrophy F-box (Fbx) 32, 40% for Fbx25, and 25% for muscle RING finger-1 (MuRF1, P < 0.05). IGF-I and insulin stimulated phosphorylation of FOXO1 and FOXO4 (P < 0.05), which was inhibited by the phosphatidylinositol 3-kinase (PI 3-kinase) inhibitor wortmannin, and decreased the abundance of polyubiquitinated proteins by 10-20% (P < 0.05). Supplementing media with leucine reduced Fbx32 expression by 25% (P < 0.05) but did not affect Fbx25 nor MuRF1 transcript abundance. Serum deprivation decreased rates of protein synthesis by 60% (P < 0.05), increased protein degradation by 40% (P < 0.05), and increased expression of all ubiquitin ligases. These data suggest that, similar to mammals, the inhibitory effects of IGF-I and insulin on proteolysis occur via P I3-kinase/protein kinase B signaling and are partially responsible for the ability of these compounds to promote protein accretion.

Digestive capacities, inbreeding and growth capacities in juvenile Arctic charr Salvelinus alpinus

Genetic variation in growth performance was estimated in 26 families from two commercial strains of Arctic charr Salvelinus alpinus. Physiological determinants of growth and metabolic capacities were also assessed through enzymatic assays. A relatedness coefficient was attributed to each family using parental genotypes at seven microsatellite loci. After 15 months of growth, faster growing families had significantly lower relatedness coefficients than slower growing families, suggesting their value as indicators of growth potential. Individual fish that exhibited higher trypsin activity also displayed higher growth rate, suggesting that superior protein digestion capacities can be highly advantageous at early stages. Capacities to use amino acids as expressed by glutamate dehydrogenase (GDH) activities were lower in the liver of fast-growing fish (13-20%), whereas white muscle of fast-growing fish showed higher activities than that of slow-growing fish for amino acid metabolism and aerobic capacity [22-32% increase for citrate synthase (CS), aspartate aminotransferase (AAT) and GDH]. The generally higher glycolytic capacities (PK and LDH) in white muscle of fast-growing fish indicated higher burst swimming capacities and hence better access to food.

Long-term prediction of fish growth under varying ambient temperature using a multiscale dynamic model

Background

Feed composition has a large impact on the growth of animals, particularly marine fish. We have developed a quantitative dynamic model that can predict the growth and body composition of marine fish for a given feed composition over a timespan of several months. The model takes into consideration the effects of environmental factors, particularly temperature, on growth, and it incorporates detailed kinetics describing the main metabolic processes (protein, lipid, and central metabolism) known to play major roles in growth and body composition.

Results

For validation, we compared our model's predictions with the results of several experimental studies. We showed that the model gives reliable predictions of growth, nutrient utilization (including amino acid retention), and body composition over a timespan of several months, longer than most of the previously developed predictive models.

Conclusion

We demonstrate that, despite the difficulties involved, multiscale models in biology can yield reasonable and useful results. The model predictions are reliable over several timescales and in the presence of strong temperature fluctuations, which are crucial factors for modeling marine organism growth. The model provides important improvements over existing models.

Insulin-like growth factor-I and genetic effects on indexes of protein degradation in response to feed deprivation in rainbow trout (Oncorhynchus mykiss)

This study determined the effect of genetic variation, feed deprivation, and insulin-like growth factor-I (IGF-I) on weight loss, plasma IGF-I and growth hormone, and indexes of protein degradation in eight full-sibling families of rainbow trout. After 2 wk of feed deprivation, fish treated with IGF-I lost 16% less (P < 0.05) wet weight than untreated fish. Feed deprivation increased growth hormone (P < 0.05) and decreased IGF-I (P < 0.05), but hormone levels were not altered by IGF-I. Plasma 3-methylhistidine concentrations were not affected by IGF-I but were decreased after 2 wk (P < 0.05) and increased after 4 wk (P < 0.05) of feed deprivation. In white muscle, transcript abundance of genes in the ubiquitin-proteasome, lysosomal, and calpain- and caspase-dependent pathways were affected by feed deprivation (P < 0.05). IGF-I prevented the feed deprivation-induced upregulation of MAFbx (F-box) and cathepsin transcripts and reduced abundance of proteasomal mRNAs (P < 0.05), suggesting that reduction of protein degradation via these pathways may be partially responsible for the IGF-I-induced reduction of weight loss. Family variations in gene expression, IGF-I concentrations, and weight loss during fasting suggest genetic variation in the fasting response, with considerable impact on regulation of proteolytic pathways. These data indicate that nutrient availability, IGF-I, and genetic variation affect weight loss, in part through alterations of proteolytic pathways in rainbow trout, and that regulation of genes within these pathways is coordinated in a way that supports a similar physiological response.

Protein synthesis is lowered while 20S proteasome activity is maintained following acclimation to low temperature in juvenile spotted wolffish(Anarhichas minor Olafsen)

The effects of temperature on protein metabolism have been studied mostly with respect to protein synthesis. Temperature generally has a parabolic effect on protein synthesis with a maximum rate being observed at optimal growth temperature. The effect of temperature on protein degradation is poorly understood. The 20S proteasome is mainly responsible for the degradation of short-lived and oxidatively modified proteins and has been recently identified as a potentially good proxy for protein degradation in fish. The aim of this experiment was to examine the relationships between the rate of protein synthesis, activity of the 20S proteasome, oxidative stress markers and antioxidant capacity in white muscle of juvenile spotted wolffish(Anarhichas minor) acclimated at three temperatures (4, 8 and 12°C). The rate of protein synthesis was lower at 4°C than at 8°C while it was intermediate at 12°C. Despite the decrease of protein synthesis at low temperature, the activity of 20S proteasome activity was maintained high in fish acclimated at lower temperature (4°C), reaching levels 130% of that of fish acclimated at 8°C when measured at a common temperature. The oxidative stress markers TBARS and protein-carbonyl content did not change among temperature groups, but reduced glutathione concentration was higher in cold-acclimated fish, suggesting a higher antioxidant capacity in this group. Our data suggest that lower growth rate in cold temperature results from both high 20S proteasome activity and a reduced rate of protein synthesis.

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.

Protein metabolism in marine animals: the underlying mechanism of growth

Growth is a fundamental process within all marine organisms. In soft tissues, growth is primarily achieved by the synthesis and retention of proteins as protein growth. The protein pool (all the protein within the organism) is highly dynamic, with proteins constantly entering the pool via protein synthesis or being removed from the pool via protein degradation. Any net change in the size of the protein pool, positive or negative, is termed protein growth. The three inter-related processes of protein synthesis, degradation and growth are together termed protein metabolism. Measurement of protein metabolism is vital in helping us understand how biotic and abiotic factors affect growth and growth efficiency in marine animals. Recently, the developing fields of transcriptomics and proteomics have started to offer us a means of greatly increasing our knowledge of the underlying molecular control of protein metabolism. Transcriptomics may also allow us to detect subtle changes in gene expression associated with protein synthesis and degradation, which cannot be detected using classical methods. A large literature exists on protein metabolism in animals; however, this chapter concentrates on what we know of marine ectotherms; data from non-marine ectotherms and endotherms are only discussed when the data are of particular relevance. We first consider the techniques available to measure protein metabolism, their problems and what validation is required. Protein metabolism in marine organisms is highly sensitive to a wide variety of factors, including temperature, pollution, seasonality, nutrition, developmental stage, genetics, sexual maturation and moulting. We examine how these abiotic and biotic factors affect protein metabolism at the level of whole-animal (adult and larval), tissue and cellular protein metabolism. Available gene expression data, which help us understand the underlying control of protein metabolism, are also discussed. As protein metabolism appears to comprise a significant proportion of overall metabolic costs in marine organisms, accurate estimates of the energetic cost per unit of synthesised protein are important. Measured costs of protein metabolism are reviewed, and the very high variability in reported costs highlighted. Two major determinants of protein synthesis rates are the tissue concentration of RNA, often expressed as the RNA to protein ratio, and the RNA activity (k(RNA)). The effects of temperature, nutrition and developmental stage on RNA concentration and activity are considered. This chapter highlights our complete lack of knowledge of protein metabolism in many groups of marine organisms, and the fact we currently have only limited data for animals held under a narrow range of experimental conditions. The potential assistance that genomic methods may provide in increasing our understanding of protein metabolism is described.

Muscle delta13C change in Nile tilapia (Oreochromis niloticus): effects of growth and carbon turnover

The contribution of growth and turnover to the muscle delta(13)C change process was investigated using mathematical models which associate delta(13)C change to time of intake of a new diet or increase in body mass. Two groups of Nile tilapia (Oreochromis niloticus) were fed on diets based on C3 (delta(13)C=-25.64+/-0.06 per thousand) or C4 (delta(13)C=-16.01+/-0.06 per thousand) photosynthetic cycle plants to standardize the muscle delta(13)C. After establishing the carbon isotopic equilibrium, fish (mean mass 24.12+/-6.79 g) then received the other treatment diet until a new carbon isotopic equilibrium could be established, characterizing T1 (C3-C4) and T2 (C4-C3) treatments. No significant differences were observed in fish productive performance. Good fits were obtained for the models that associated the delta(13)C change to time, resulting in carbon half-life values of 23.33 days for T1 and 25.96 days for T2. Based on values found for the muscle delta(13)C change rate from growth (0.0263 day(-1) and 0.0254 day(-1)) and turnover (0.0034 day(-1) and 0.0013 day(-1)), our results indicate that most of the delta(13)C change could be attributed to growth. The application of model that associated the delta(13)C change to body mass increase seems to produce results with no apparent biological explanation. The delta(13)C change rate could directly reflect the daily ration and growth rate, and consequently the isotopic change rates of carbon and other tissue elements can be properly used to assess different factors that may interfere in nutrient utilization and growth.

Anabolic effects of feeding beta2-adrenergic agonists on rainbow trout muscle proteases and proteins

beta2-Adrenergic agonists (BAAs) act as repartitioning agents in domestic animals by redistributing nutrients away from adipose tissue and towards muscle accretion. The mechanism involves altering the rates of protein degradation and synthesis. The aim of this study was to test the effects of chronic feeding of the BAAs clenbuterol (CLEN) and ractopamine (RACT) on rainbow trout (RBT) muscle. Specifically, we examined the activities and mRNA levels of genes in the major proteolytic pathways including calpains, the multi-catalytic proteasome and cathepsins, and the mRNA levels of genes encoding the myofibrillar proteins, fast-twitch and slow-twitch myosin heavy chains (f-MHC and s-MHC, respectively), and the cytoskeletal protein, beta-actin. RACT feeding significantly increased mRNA transcripts of the calpain catalytic subunit (Capn1), the regulatory subunit (cpns), and the calpastatin large isoform (CAST-L), without affecting the calpain enzyme activity. CLEN feeding significantly increased mRNA levels of the proteasome alpha subunit without a corresponding change in 20S enzyme activity. RACT significantly decreased cathepsin D activity without affecting mRNA levels suggesting that the action of RACT may be at the post-transcriptional level. In addition, both CLEN and RACT significantly increased mRNA transcripts of f-MHC and beta-actin genes suggesting an anabolic role of BAAs on myofibrillar and cytoskeletal proteins. Neither CLEN nor RACT altered mRNA expression of the s-MHC gene indicating no transformation of muscle fiber-types. This study supports a role for BAAs in inducing RBT muscle accretion by altering both protein synthesis and degradation.

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

Severe muscle deterioration is a physiological response to the energetic demands of fish spawning. This response represents a suitable model to study mechanisms of muscle degradation in fish where typical tetrapod methods, such as muscle unloading, are not applicable. Enzyme activities and mRNA accumulations of genes in major proteolytic pathways, including cathepsins, calpains and the multi-catalytic proteasome, were measured in white muscles of rainbow trout during spawning and post-spawning seasons of gravid fish for comparisons to sterile fish. Fertile fish at spawning had less muscle tissue and less muscle protein compared to sterile fish and post-spawning fertile fish. Muscle deterioration of the fertile fish during spawning was associated with greater mRNA accumulation and elevated activity of cathepsin-L. Concurrently, muscle of spawning fish showed increased mRNA accumulations of cathepsin-D, the calpain regulatory subunit and the proteasome catalytic subunit alpha without corresponding increases in enzyme activities. In addition, elevated activity and increased mRNA accumulation of caspase-9, but not caspase-3, were observed in fertile fish during spawning. This study indicates that cathepsins mediate protein catabolism during spawning in rainbow trout and the catabolic process may involve activation of the apoptosis mediator, caspase-9, but not the apoptosis executioner, caspase-3.

The Subunit Structure and Dynamics of the 20S Proteasome in Chicken Skeletal Muscle

We have succeeded in purifying the 20S core proteasome particle from less than 1 g of skeletal muscle in a rapid process involving two chromatographic steps. The individual subunits were readily resolved by two-dimensional PAGE, and the identities of each of the 14 subunits were assigned by a combination of peptide mass fingerprinting and MS/MS/de novo sequencing. To assess the dynamics of proteasome biogenesis, chicks were fed a diet containing stable isotope-labeled valine, and the rate of incorporation of label into valine-containing peptides derived from each subunit was assessed by mass spectrometric analysis after two-dimensional separation. Peptides containing multiple valine residues from the 20S proteasome and other soluble muscle proteins were analyzed to yield the relative isotope abundance of the precursor pool, a piece of information that is essential for calculation of turnover parameters. The rates of synthesis of each subunit are rather similar, although there is evidence for high turnover subunits in both the alpha (nonproteolytic) and beta (proteolytic) rings. The variability in synthesis rate for the different subunits is consistent with a model in which some subunits are produced in excess, whereas others may be the rate-limiting factor in the concentration of 20S subunits in the cell. The ability to measure turnover rates of proteins on a proteome-wide scale in protein assemblies and in a complex organism provides a new dimension to the understanding of the dynamic proteome.

Dietary plant-protein substitution affects hepatic metabolism in rainbow trout (Oncorhynchus mykiss)

The high dietary protein requirements of salmonid fish are met with fishmeal-based feed in commercial aquaculture. The sustainability of this practice is questionable and, therefore, the feasibility of substituting fishmeal with plant-based products needs to be investigated. We investigated growth and metabolism in rainbow trout (Oncorhynchus mykiss) fed a diet composed of a mixture of plant proteins compared with those fed a fishmeal-based diet. Using two-dimensional gel electrophoresis of liver protein extracts, we showed that the liver protein profile changed in response to the alteration in the diet. A number of metabolic pathways were identified as sensitive to the protein source substitution. These included pathways involved in primary energy generation, maintenance of reducing potential, bile acid synthesis, and transport and cellular protein degradation. Interestingly, the pathways shown to be affected in the present study were somewhat different from those identified in our previous work with soyabean-based-protein replacement of fishmeal, with the effects on the abundance of several stress response proteins notably absent. We conclude, therefore, that the metabolic effects of plant protein replacement in aquaculture feed varies with plant-protein source.