Methionine is an indispensable amino acid with an important role as the main methyl donor in cellular metabolism for both fish and mammals. Metabolization of methionine to the methyl donor S-adenosylmethionine (SAM) has consequence for polyamine, carnitine, phospholipid, and creatine synthesis as well as epigenetic modifications such as DNA- and histone tail methylation. Methionine can also be converted to cysteine and contributes as a precursor for taurine and glutathione synthesis. Moreover, methionine is the start codon for every protein being synthetized and thereby serves an important role in initiating translation. Modern salmon feed is dominated by plant ingredients containing less taurine, carnitine, and creatine than animal-based ingredients. This shift results in competition for SAM due to an increasing need to endogenously synthesize associated metabolites. The availability of methionine has profound implications for various metabolic pathways including allosteric regulation. This necessitates a higher nutritional need to meet the requirement as a methyl donor, surpassing the quantities for protein synthesis and growth. This comprehensive review provides an overview of the key metabolic pathways in which methionine plays a central role as methyl donor and unfolds the implications for methylation capacity, metabolism, and overall health particularly emphasizing the development of fatty liver, oxidation, and inflammation when methionine abundance is insufficient focusing on nutrition for Atlantic salmon (Salmo salar).

Diet has been shown to influence epigenetic key players, such as DNA methylation, which can regulate the gene expression potential in both parents and offspring. Diets enriched in omega-6 and deficient in omega-3 PUFAs (low dietary omega-3/omega-6 PUFA ratio), have been associated with the promotion of pathogenesis of diseases in humans and other mammals. In this study, we investigated the impact of increased dietary intake of arachidonic acid (ARA), a physiologically important omega-6 PUFA, on 2 generations of zebrafish. Parental fish were fed either a low or a high ARA diet, while the progeny of both groups were fed the low ARA diet. We screened for DNA methylation on single base-pair resolution using reduced representation bisulfite sequencing (RRBS). The DNA methylation profiling revealed significant differences between the dietary groups in both parents and offspring. The majority of differentially methylated loci associated with high dietary ARA were found in introns and intergenic regions for both generations. Common loci between the identified differentially methylated loci in F₀ and F₁ livers were reported. We described overlapping gene annotations of identified methylation changes with differential expression, but based on a small number of overlaps. The present study describes the diet-associated methylation profiles across genomic regions, and it demonstrates that parental high dietary ARA modulates DNA methylation patterns in zebrafish liver.

Disproportionate high intake of n-6 polyunsaturated fatty acids (PUFAs) in the diet is considered as a major human health concern. The present study examines changes in the hepatic gene expression pattern of adult male zebrafish progeny associated with high levels of the n-6 PUFA arachidonic acid (ARA) in the parental diet. The parental generation (F₀) was fed a diet which was either low (control) or high in ARA (high ARA). Progenies of both groups (F₁) were given the control diet. No differences in body weight were found between the diet groups within adult stages of either F₀ or F₁ generation. Few differentially expressed genes were observed between the two dietary groups in the F₀ in contrast to the F₁ generation. Several links were found between the previous metabolic analysis of the parental fish and the gene expression analysis in their adult progeny. Main gene expression differences in the progeny were observed related to lipid and retinoid metabolism by PPARα/RXRα playing a central role in mediating changes to lipid and long-chain fatty acid metabolism. The enrichment of genes involved in β-oxidation observed in the progeny, corresponded to the increase in peroxisomal β-oxidative degradation of long-chain fatty acids in the parental fish metabolomics data. Similar links between the F₀ and F₁ generation were identified for the methionine cycle and transsulfuration pathway in the high ARA group. In addition, estrogen signalling was found to be affected by parental high dietary ARA levels, where gene expression was opposite directed in F₁ compared to F₀. This study shows that the dietary n-3/n-6 PUFA ratio can alter gene expression patterns in the adult progeny. Whether the effect is mediated by permanent epigenetic mechanisms regulating gene expression in developing gametes needs to be further investigated.

A moderate surplus of the one carbon (1C) nutrients methionine, folic acid, vitamin B ₆ and B ₁₂ above dietary recommendations for Atlantic salmon has shown to improve growth and reduce hepatosomatic index in the on-growing saltwater period when fed throughout smoltification. Metabolic properties and molecular mechanisms determining the improved growth are unexplored. Here, we investigate metabolic and transcriptional signatures in skeletal muscle taken before and after smoltification to acquire deeper insight into pathways and possible nutrient–gene interactions. A control feed (Ctrl) or 1C nutrient surplus feed (1C+) were fed to Atlantic salmon 6 weeks prior to smoltification until 3 months after saltwater transfer. Both metabolic and gene expression signatures revealed significant 1C nutrient-dependent changes already at pre-smolt, but differences intensified when analysing post-smolt muscle. Transcriptional differences revealed lower expression of genes related to translation, growth and amino acid metabolisation in post-smolt muscle when fed additional 1C nutrients. The 1C+ group showed less free amino acid and putrescine levels, and higher methionine and glutathione amounts in muscle. For Ctrl muscle, the overall metabolic profile suggests a lower amino acid utilisation for protein synthesis, and increased methionine metabolisation in polyamine and redox homoeostasis, whereas transcription changes are indicative of compensatory growth regulation at local tissue level. These findings point to fine-tuned nutrient–gene interactions fundamental for improved growth capacity through better amino acid utilisation for protein accretion when salmon was fed additional 1C nutrients throughout smoltification. It also highlights potential nutritional programming strategies on improved post-smolt growth through 1C+ supplementation before and throughout smoltification.

Supplementation of one-carbon (1C) metabolism micronutrients, which include B-vitamins and methionine, is essential for the healthy growth and development of Atlantic salmon (Salmo salar). However, the recent shift towards non-fish meal diets in salmon aquaculture has led to the need for reassessments of recommended micronutrient levels. Despite the importance of 1C metabolism in growth performance and various cellular regulations, the molecular mechanisms affected by these dietary alterations are less understood. To investigate the molecular effect of 1C nutrients, we analysed gene expression and DNA methylation using two types of omics data: RNA sequencing (RNA-seq) and reduced-representation bisulphite sequencing (RRBS). We collected liver samples at the end of a feeding trial that lasted 220 days through the smoltification stage, where fish were fed three different levels of four key 1C nutrients: methionine, vitamin B6, B9, and B12. Our results indicate that the dosage of 1C nutrients significantly impacts genetic and epigenetic regulations in the liver of Atlantic salmon, particularly in biological pathways related to protein synthesis. The interplay between DNA methylation and gene expression in these pathways may play an important role in the mechanisms underlying growth performance affected by 1C metabolism.

The metabolic pathway of vitamin D3 is well characterized in mammals, but its genetic basis in teleost fish remains poorly defined. We identified 16 vitamin D3-related genes in Atlantic salmon ( Salmo salar ), 14 orthologs of pathway genes and two albumins as candidate carriers, and profiled their expression in a 14-tissue atlas and in seven independent RNA-seq studies. Phylogenetic analysis resolved seven paralog pairs from the salmonid whole-genome duplication. Atlantic salmon and three other euteleost fishes lacked a gc gene, and the genes that flank gc in other fishes were adjacent in their genomes. The proteins annotated as GC in three Oncorhynchus species were albumins. Skin expression of dhcr7 , which converts the precursor 7-dehydrocholesterol to cholesterol, was low and differed between studies. The activating enzyme cyp27b1 was barely expressed in five kidney and 21 head kidney samples, including those of the atlas, whereas cyp27b1.a was expressed in the brain and cyp27b1.b in the liver. In northern pike, which lacks this duplication, cyp27b1 was not detected in the kidney either. The catabolic enzyme cyp24a1 was only weakly expressed in the kidney and the head kidney. These transcript data suggest that vitamin D3 activation in Atlantic salmon may not depend on renal cyp27b1 expression under the conditions sampled, and that albumins or lipoproteins may carry vitamin D metabolites. Both hypotheses need to be tested with protein, enzyme activity, and metabolite measurements. The curated gene set provides a basis for studies of vitamin D3 metabolism and dietary vitamin D3 requirements in salmonids.