Micronutrient supplementation affects transcriptional and epigenetic regulation of lipid metabolism in a dose-dependent manner

Micronutrients (vitamins and minerals) have been less well studied compared to macronutrients (fats, proteins, and carbohydrates) although they play important roles in growth, metabolism, and maintenance of tissues. Hence, there is growing interest to understand the influence of micronutrients across various aspects in nutritional research. In the last two decades, aquaculture feeds have been shifted to containing more plant-based materials to meet the increasing demand and maintain the sustainability in the industry. In cultured fish, changing raw materials in feeds alters the requirement levels of micronutrients. A recent whole life cycle feeding trial of Atlantic salmon (Salmo salar) with graded levels of micronutrient packages has concluded that the levels of several B-vitamins and microminerals need to be increased from the current recommendation levels for optimal growth and fish welfare when plant-based diets are used. Here, we show the effect of micronutrient supplementation on transcriptional and epigenetic regulation by using liver samples from the same feeding trial. Specifically, our aim is to reveal the mechanisms of altered cell metabolism, which results in improved growth performance by micronutrient surpluses, at gene expression and DNA methylation levels. Our results strongly indicate that micronutrient supplementation suppresses gene expression in lipid metabolism in a dose-dependent manner and broadly affects DNA methylation in cell adhesion and cell signalling. In particular, it increases DNA methylation levels on the acetyl-CoA carboxylase alpha promoter in a concentration-dependent manner, which further suggests that acetyl-CoA carboxylase alpha is an upstream epigenetic regulator controlling its downstream lipid biosynthesis activities. This study demonstrates a comprehensive analysis to reveal an important role of micronutrients in lipid metabolism through epigenetic control of gene expression

The apoptosis-inducing activity towards leukemia and lymphoma cells in a cyanobacterial culture collection is not associated with mouse bioassay toxicity

Cyanobacteria (83 strains and seven natural populations) were screened for content of apoptosis (cell death)-inducing activity towards neoplastic cells of the immune (jurkat acute T-cell lymphoma) and hematopoetic (acute myelogenic leukemia) lineage. Apoptogenic activity was frequent, even in strains cultured for decades, and was unrelated to whether the cyanobacteria had been collected from polar, temperate, or tropic environments. The activity was more abundant in the genera Anabaena and Microcystis compared to Nostoc, Phormidium, Planktothrix, and Pseudanabaena. Whereas the T-cell lymphoma apoptogens were frequent in organic extracts, the cell death-inducing activity towards leukemia cells resided mainly in aqueous extracts. The cyanobacteria were from a culture collection established for public health purposes to detect toxic cyanobacterial blooms, and 54 of them were tested for toxicity by the mouse bioassay. We found no correlation between the apoptogenic activity in the cyanobacterial isolates with their content of microcystin, nor with their ability to elicit a positive standard mouse bioassay. Several strains produced more than one apoptogen, differing in biophysical or biological activity. In fact, two strains contained microcystin in addition to one apoptogen specific for the AML cells, and one apoptogen specific for the T-cell lymphoma. This study shows the potential of cyanobacterial culture collections as libraries for bioactive compounds, since strains kept in cultures for decades produced apoptogens unrelated to the mouse bioassay detectable bloom-associated toxins

Mitochondrial DNA methylation profiling in Nile tilapia (Oreochromis niloticus) through nanopore sequencing

6th International Symposium on Genomics in Aquaculture (GIA 2022), 4-6 May 2022, GranadaThe mitochondrion is a cellular organelle that plays a central role in the regulation of respiration and metabolic processes in the cell. Thus, it is implicated in growth, metabolism and aging of an organism. The first study on mitochondrial DNA (mtDNA) epigenetics have been published at the beginning of the 1970s (Nass, 1973). The identification of DNA methyltransferase 1 in mammalian mitochondria attracted researchers towards the study of the mitoepigenome (Shock et al., 2011). However, data about the methylation patterns of mtDNA in adult fish tissues is still absent, apart from a single report (Nedoluzhko et al., 2021). Mitochondria play a critical role in the production of reactive oxygen species, which in turn is essential for muscle function and growth. Growth is one of the most important traits in the aquaculture sector (Gjedrem, 2005). In the present study, mtDNA methylation profiles have been analysed in Nile tilapia (Oreochromis niloticus), fast muscle using Nanopore long-read sequencing. O. niloticus fast tissue was sampled, and used for genomic DNA isolation and construction of PCR-free libraries. The Nanopore MinION Mk1C sequencing workflow generated 673 Fast5 files, which were used for basecalling and methylation analysis with Megalodon v2.4.2 and Remora v0.1.2. The mean sequencing read length was 3275 bp and the coverage obtained for Nile tilapia mtDNA was 1082X. This methylation data analysis based on Nanopore long-read sequencing constitutes a valuable resource for future research on the mitoepigenome of farmed fishes. References: Gjedrem, T. (2005). Selection and Breeding Programs in Aquaculture: Springer Netherlands. Nass, M.M. (1973). Differential methylation of mitochondrial and nuclear DNA in cultured mouse, hamster and virus-transformed hamster cells in vivo and in vitro methylation. Journal of Molecular Biology, 80(1), 155-175. Nedoluzhko, A., Mjelle, R., Renström, M., Skjærven, K.H., Piferrer, F., and Fernandes, J.M.O. (2021). The first mitochondrial 5-methylcytosine map in a non-model teleost (Oreochromis niloticus) reveals extensive strand-specific and non-CpG methylation. Genomics, 113, 3050-3057. Shock, L.S., Thakkar, P.V., Peterson, E.J., Moran, R.G., and Taylor, S. M. (2011). DNA methyltransferase 1, cytosine methylation, and cytosine hydroxymethylation in mammalian mitochondria. Proceedings of the National Academy of Sciences, 108(9), 3630-3635This work was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no 683210) and by the Research Council of Norway under the Toppforsk programme (grant agreement no 250548/F20), with additional support from Notur/NorStore (project NN9337K)Peer reviewe

Nanopore sequencing reveals growth rates-dependent differential methylation of the mitogenome in Nile tilapia (Oreochromis niloticus) muscle

Aquaculture Europe 22, Innovative solutions in a changing world, 27-30 September 2022, Rimini, ItalyThe mitochondrion is a cellular organelle that plays a central role in the regulation of respiration and metabolic processes in the cell, which are essential for muscle function and growth. Mitochondrial efficiency is directly linked with growth rate and varies among individuals, but the molecular basis of these differences is currently unknown. The aim of this study was to investigate a potential link between mtDNA methylation and growth rates in Nile tilapia (Oreochromis niloticus) muscle, since we have reported that the liver mitogenome is 20 % methylated (25 % CpGs) in this species. (Nedoluzhko et al., 2021). Fast muscle was sampled from slow and fast-growing Nile tilapia males and females, and used for genomic DNA isolation and construction of PCR-free libraries. In a representative library, the Nanopore MinION Mk1C sequencing workflow generated 673 Fast5 files, which were used for basecalling and methylation analysis with Megalodon v2.4.2 and Remora v0.1.2. The mean sequencing read length was 3275 bp and the coverage obtained for Nile tilapia mtDNA was 1082X. Methylation data generated from Nanopore long-read sequencing constitute a valuable resource for future research on the mitoepigenome related to muscle growth, metabolism and oxidation status of farmed fishesReferences: Nedoluzhko, A., Mjelle, R., Renström, M., Skjærven, K.H., Piferrer, F., and Fernandes, J.M.O. (2021). The first mitochondrial 5-methylcytosine map in a non-model teleost (Oreochromis niloticus) reveals extensive strand-specific and non-CpG methylation. Genomics, 113, 3050-3057This work was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no 683210) and by the Research Council of Norway under the Toppforsk programme (grant agreement no 250548/F20), with additional support from Notur/NorStore (project NN9337K)Peer reviewe

The mitochondrial 5-methylcytosine profile in Nile tilapia (Oreochromis niloticus)

6th International Symposium on Genomics in Aquaculture (GIA), 5-7 May 2021Growth and metabolism are closely linked to mitochondrion, since this organelle¿s primary function is generation of cellular energy by production of ATP (adenosine triphosphate). Mitochondrion has a compact circular genome (16,5 Kb in average), which is related to its bacterial origin. The mitogenome in Nile tilapia (Oreochromis niloticus) is 16,625 bp long and contains 13 protein-coding genes (involved in oxidative phosphorylation), two rRNA genes, 22 tRNA genes and the D-loop (putative control region). The number and the order of mitochondrial genes in Nile tilapia matches those in other cichlids. DNA methylation is one of several epigenetic regulatory mechanisms that control gene expression. In fish, epigenetic changes associated with mtDNA and their potential relation to functional effects on growth is still a question that remains unanswered. In this study, we isolated mtDNA from liver of 5 full-sib Nile tilapia females. A whole genome bisulfite sequencing (Illumina NextSeq) approach was used for identifying methylation patterns within CHH, CHG and CpG context in the mitochondrial genome. We described and compared methylation rate among mitochondrial genes to create the first methylome map of mtDNA in fish. Our results demonstrated the presence of mtDNA methylation in fish, predominantly within non-CpG context. We found a strand-specific distribution of mtDNA methylation, where most of methylated cytosines were located on the light (minus) strand. The D-loop region had the highest mean methylation value among all mitochondrial genes. These data provide a new insight into mitochondrial epigenetics in fish and can serve as a background for further functional investigation of potential epigenetic markers involved in shaping metabolic flexibility and growth in Nile tilapi

The effect of micronutrient supplementation on growth and hepatic metabolism in diploid and triploid Atlantic salmon (Salmo salar) parr fed a low marine ingredient diet

The effects of low marine ingredient diets supplemented with graded levels (L1, L2, L3) of a micronutrient package (NP) on growth and metabolic responses were studied in diploid and triploid salmon parr. Diploids fed L2 showed significantly improved growth and reduced liver, hepatic steatosis, and viscerosomatic indices, while fish fed L3 showed suppressed growth rate 14 weeks post feeding. In contrast, dietary NP level had no effect on triploid performance. Whole body mineral composition, with exception of copper, did not differ between diet or ploidy. Whole fish total AAs and N-metabolites showed no variation by diet or ploidy. Free circulating AAs and white muscle N-metabolites were higher in triploids than diploids, while branch-chained amino acids were higher in diploids than triploids. Diploids had higher whole body α-tocopherol and hepatic vitamins K1 and K2 than triploids. Increased tissue B-vitamins for niacin and whole-body folate with dietary NP supplementation were observed in diploids but not triploids, while whole body riboflavin was higher in diploids than triploids. Hepatic transcriptome profiles showed that diploids fed diet L2 was more similar to that observed in triploids fed diet L3. In particular, sterol biosynthesis pathways were down-regulated, whereas cytochrome P450 metabolism was up-regulated. One‑carbon metabolism was also affected by increasing levels of supplementation in both ploidies. Collectively, results suggested that, for optimised growth and liver function, micronutrient levels be supplemented above current National Research Council (2011) recommendations for Atlantic salmon when fed low marine ingredient diets. The study also suggested differences in nutritional requirements between ploidy