Early leucine programming on protein utilization and mTOR signaling by DNA methylation in zebrafish (Danio rerio)

Broodstock nutritional programming differentially affects the hepatic transcriptome and genome-wide DNA methylome of farmed gilthead sea bream (Sparus aurata) depending on genetic background

BACKGROUND

Broodstock nutritional programming improves the offspring utilization of plant-based diets in gilthead sea bream through changes in hepatic metabolism. Attention was initially focused on fatty acid desaturases, but it can involve a wide range of processes that remain largely unexplored. How all this can be driven by a different genetic background is hardly underlined, and the present study aimed to assess how broodstock nutrition affects differentially the transcriptome and genome-wide DNA methylome of reference and genetically selected fish within the PROGENSA® selection program.

RESULTS

After the stimulus phase with a low fish oil diet, two offspring subsets of each genetic background received a control or a FUTURE-based diet. This highlighted a different hepatic transcriptome (RNA-seq) and genome-wide DNA methylation (MBD-seq) pattern depending on the genetic background. The number of differentially expressed transcripts following the challenge phase varied from 323 in reference fish to 2,009 in genetically selected fish. The number of discriminant transcripts, and associated enriched functions, were also markedly higher in selected fish. Moreover, correlation analysis depicted a hyper-methylated and down-regulated gene expression state in selected fish with the FUTURE diet, whereas the opposite pattern appeared in reference fish. After filtering for highly represented functions in selected fish, 115 epigenetic markers were retrieved in this group. Among them, lipid metabolism genes (23) were the most reactive following ordering by fold-change in expression, rendering a final list of 10 top markers with a key role on hepatic lipogenesis and fatty acid metabolism (cd36, pitpna, cidea, fasn, g6pd, lipt1, scd1a, acsbg2, acsl14, acsbg2).

CONCLUSIONS

Gene expression profiles and methylation signatures were dependent on genetic background in our experimental model. Such assumption affected the magnitude, but also the type and direction of change. Thus, the resulting epigenetic clock of reference fish might depict an older phenotype with a lower methylation for the epigenetically responsive genes with a negative methylation-expression pattern. Therefore, epigenetic markers will be specific of each genetic lineage, serving the broodstock programming in our selected fish to prevent and mitigate later in life the risk of hepatic steatosis through changes in hepatic lipogenesis and fatty acid metabolism.

Effect of Early Peptide Diets on Zebrafish Skeletal Development

Incorporation of dietary peptides has been correlated with decreased presence of skeletal abnormalities in marine larvae. In an attempt to clarify the effect of smaller protein fractions on fish larval and post-larval skeleton, we designed three isoenergetic diets with partial substitution of their protein content with 0% (C), 6% (P6) and 12% (P12) shrimp di- and tripeptides. Experimental diets were tested in zebrafish under two regimes, with inclusion (ADF-Artemia and dry feed) or lack (DF-dry feed only) of live food. Results at the end of metamorphosis highlight the beneficial effect of P12 on growth, survival and early skeletal quality when dry diets are provided from first feeding (DF). Exclusive feeding with P12 also increased the musculoskeletal resistance of the post-larval skeleton against the swimming challenge test (SCT). On the contrary, Artemia inclusion (ADF) overruled any peptide effect in total fish performance. Given the unknown species' larval nutrient requirements, a 12% dietary peptide incorporation is proposed for successful rearing without live food. A potential nutritional control of the larval and post-larval skeletal development even in aquaculture species is suggested. Limitations of the current molecular analysis are discussed to enable the future identification of the peptide-driven regulatory pathways.

Whole-genome resequencing and bisulfite sequencing provide new insights into the feeding habit domestication in mandarin fish (Siniperca chuatsi)

Mandarin fish (Siniperca chuatsi) is one of the most economically important fish in China. However, it has the peculiar feeding habit that it feeds solely on live prey fish since first-feeding, while refuses dead prey fish or artificial diets. After the specific training procedure, partial individuals could accept dead prey fish and artificial diets. The genetic basis of individual difference in artificial diet feeding habit is still unknown. In the present study, the resequencing was performed between 10 individuals which could be domesticated to accept artificial diets and 10 individuals which could not. Through the selective sweep analysis based on heterozygosity (Hp) and population differentiation coefficient (Fst), 57 candidate windows were identified as the putative selected regions for feeding habit domestication of mandarin fish, involved in 149 genes. These genes were related to memory, vision and olfaction function, which could be potential targets of molecular marker assistant breeding of artificial diet feeding trait. Beside of the DNA sequence, we also explored the potential role of DNA methylation in feeding habit domestication in mandarin fish. Whole-genome bisulfite sequencing was performed between the individuals which could be domesticated to accept artificial diets and those could not. 5,976 differentially methylated regions were identified, referring to 3,522 genes, such as the genes involved in cAMP signaling pathway. The DNA methylation changes of these genes might contribute to the adaption of artificial diets in mandarin fish. In conclusion, the putative selected regions and the differentially methylated regions were identified in the whole genome, providing new insights into the feeding habit domestication from live prey fish to artificial diets in mandarin fish. And the involved genes were identified as the candidate genes for molecular breeding of artificial diet utilization in mandarin fish.

Involvement of Mechanistic Target of Rapamycin (mTOR) in Valine Orexigenic Effects in Rainbow Trout

This study was aimed at clarifying the importance of a mechanistic target of rapamycin (mTOR) in the central orexigenic effect of valine in fish. For this, rainbow trout (Oncorhynchus mykiss) were intracerebroventricularly (ICV) injected with valine alone or in the presence of rapamycin as the mTOR inhibitor, and two experiments were performed. In the first experiment, we evaluated feed intake levels. In the second experiment, we evaluated in the hypothalamus and telencephalon the following: (1) the phosphorylation status of mTOR and its downstream effectors ribosomal protein S6 and p70 S6 kinase 1 (S6K1), (2) the abundance and phosphorylation status of transcription factors involved in appetite regulation, and (3) the mRNA levels of key neuropeptides associated with homeostatic regulation of feed intake in fish. Rising central levels of valine clearly resulted in an orexigenic response in rainbow trout. This response occurred in parallel with mTOR activation in both the hypothalamus and telencephalon, as supported by depressant changes in proteins involved in mTOR signalling (S6 and S6K1). Also, these changes disappeared in the presence of rapamycin. However, it is not clear which precise mechanisms link the activation of mTOR and the alteration in feed intake levels since we did not observe changes in mRNA levels of appetite-regulatory neuropeptides as well as in the phosphorylation status and levels of integrative proteins.

Nutritional programming of large yellow croaker (Larimichthys crocea) larvae by dietary vegetable oil: effects on growth performance, lipid metabolism and antioxidant capacity

The nutritional status experienced in the early development of life plays a vital role in the long-term metabolic state of the individual, which is known as nutritional programming. The present study investigated the long-term effects of vegetable oil (VO) nutritional programming during the early life of large yellow croaker. First, larvae were fed either a fish oil (FO) diet or a VO diet for 30 d. Subsequently, under the same conditions, all fish were fed a commercial diet for 90 d and thereafter challenged with an FO or VO diet for 30 d. The results showed that growth performance was significantly lower in larvae fed the VO diet than in those in fed the FO diet in the stimulus phase. Notably, VO nutritional history fish showed lower levels of liver lipids liver total triglycerides and serum nonesterified free fatty acids than the FO nutritional history fish when juveniles were challenged with the VO diet, which was consistent with the expression of lipogenesis-related genes and proteins. Moreover, the VO nutritional history fish showed lower liver damage and higher antioxidant capacity than FO nutritional history fish when challenged with the VO diet. In summary, this study showed that a short VO stimulus during the early life stage of large yellow croaker, had a long-term effect on lipid metabolism and the antioxidant system. Specifically, VO nutritional programming had a positive effect on alleviating abnormal lipid deposition on the liver, liver damage, and the reduction of hepatic antioxidant capacity caused by a VO diet.

Intermittent Leucine Deprivation Produces Long-lasting Improvement in Insulin Sensitivity by Increasing Hepatic Gcn2 Expression

Leucine deprivation improves insulin sensitivity; however, whether and how this effect can be extended are unknown. We hypothesized that intermittent leucine deprivation (ILD) might produce a long-term effect on improved insulin sensitivity via the formation of metabolic memory. Consistently, seven ILD cycles of treatment (1-day leucine-deficient diet, 3-day control diet) in mice produced a long-lasting (after a control diet was resumed for 49 days) effect on improved whole-body and hepatic insulin sensitivity in mice, indicating the potential formation of metabolic memory. Furthermore, the effects of ILD depended on hepatic general control nondepressible 2 (GCN2) expression, as verified by gain- and loss-of-function experiments. Moreover, ILD increased Gcn2 expression by reducing its DNA methylation at two CpG promoter sites controlled by demethylase growth arrest and DNA damage inducible b. Finally, ILD also improved insulin sensitivity in insulin-resistant mice. Thus, ILD induces long-lasting improvements in insulin sensitivity by increasing hepatic Gcn2 expression via a reduction in its DNA methylation. These results provide novel insights into understanding of the link between leucine deprivation and insulin sensitivity, as well as potential nutritional intervention strategies for treating insulin resistance and related diseases. We also provide evidence for liver-specific metabolic memory after ILD and novel epigenetic mechanisms for Gcn2 regulation.

Appropriate leucine supplementation promotes glucose metabolism and enhances energy homeostasis in juvenile crucian carp (Carassius auratus gibelio var. CAS III)

In order to characterize the molecular mechanisms by which leucine regulates carbohydrate metabolism and energy homeostasis, juvenile crucian carps (Carassius auratus gibelio var. CAS III) fed with a high carbohydrate diet were supplemented with different levels of dietary leucine: 0% (Leu0), 0.4% (Leu4), 0.8% (Leu8), 1.2% (Leu12), 1.6% (Leu16), 2.0% (Leu20), and 5.0% (Leu50). After 8 weeks, RNA sequencing was performed on samples collected from the Leu0, Leu8, Leu12 and Leu50 groups. Differentially expressed genes were then detected and analyzed. The results showed a total of 91.6 Gb of clean bases were generated. Moreover, a total of 1131, 5254, and 1539 DEGs were detected in Leu8, Leu12, and Leu50 compared with Leu0, respectively, encompassing 161 common DEGs. STEM analysis elucidated four significant clusters of DEGs that were associated with "glycerophospholipid metabolism," "glycerolipid metabolism," "PPAR signaling pathway," and "adipocytokine signaling pathway." Moreover, the mRNA expression levels of acyl-CoA synthetase long chain family member 5 (ACSL5), choline kinase beta (CHKB), cryptochrome-1 (CRY1), lon protease homolog 2, peroxisomal isoform X2 (LONP2), lipin 1 (LPIN1), membrane bound O-acyltransferase domain containing 2 (MBOAT2), phosphoenolpyruvate carboxykinase 1 (PEPCK), and uridine-cytidine kinase 2b (UCK2b) were then further investigated in all leucine treatment groups at starvation times of 0 h, 24 h, and 48 h. The results revealed that the expression levels of UCK2b and MBOAT2 were negatively correlated with the addition of leucine, whereas CHKB, LONP2, CRY1, PEPCK, and LPIN1 were positively correlated. In conclusion, dietary leucine supplementation below 1.2% enhanced carbohydrate metabolism in juvenile crucian carp fed with a high-carbohydrate diet, whereas concentrations above 2.0% is a better choice for energy homeostasis under starvation.