Improved lipid production and transcriptomic profiling in Crypthecodinium cohnii with alternative ethanol treatment
Ontology highlight
ABSTRACT:
ORGANISM(S): Crypthecodinium cohnii
PROVIDER: GSE316578 | GEO | 2026/01/20
REPOSITORIES: GEO
Similar Datasets
Project description:This model is a supplementary material of publication
“Kinetic and stoichiometric modeling-based analysis of do-cosahexaenoic acid (DHA) production potential by C.cohnii from glycerol, glucose and ethanol”
by Kristaps Berzins, Reinis Muiznieks, Matiss R. Baumanis, Inese Strazdina, Karlis Shvirksts, Santa Prikule, Vytautas Galvanauskas, Daniel Pleissner, Agris Pentjuss, Mara Grube, Uldis Kalnenieks and Egils Stalidzans
This is a kinetic model of Crypthecodinium cohnii central carbon metabolism during fatty acid synthesis. The model is aimed at cytosolic acetyl coenzyme-A production, which is the precursor of fatty acids.
The model contains 35 reactions and 36 species split into three compartments – extracellular, cytosol and mitochondria. It was assumed that dry weight accounts for 33% of wet weight and that 1ml = 1g. The mitochondria volume is 1% of cytosol volume. The model was designed for ethanol as a single substrate. For use of glucose and glycerol as substrates, see MODEL2112280001.
The model is preset for steady state calculation using ethanol.
The model contains 31 global quantities which were used to optimize the model during parameter estimation. These global quantities include amino acid concentrations for each enzyme, the total amino acid concentration used in enzymes, the sum transport reaction variable parameters and the total concentration of species.
All enzymatic reactions contain a parameter k, which can be used for change of enzyme expression levels in case of optimization of product flux or yield. Currently all the parameters k are set for 1, which corresponds to wild-type.
The model was made for steady-state. For ethanol as a substrate a steady-state resolution of 0.1 can be used.
2022-05-06 | MODEL2112290001 | BioModels
Project description:We report the miRNA profile of murine macrophages (cell line: RAW264.7) after supplementation with polyunsaturated fatty acids (PUFA) and stimulation with LTA. The fatty acids docosahexaenoic acid (DHA, C22:6n3) or arachidonic acid (AA, C20:4n6) were included in the culture medium in concentrations of 15 µmol/L using ethanol as a vehicle (0.2 % v/v final ethanol concentration). Cells were cultured in the enriched media totaling 72 h. Stimulation of cells was performed in the last 24 h of fatty acid supplementation by addition of LTA (0.5 µg/mL; from Staphylococcus aureus).
2022-03-03 | GSE162995 | GEO
Project description:We report the transcriptome profile of murine macrophages (cell line: RAW264.7) after supplementation with polyunsaturated fatty acids (PUFA) and stimulation with LTA. The fatty acids docosahexaenoic acid (DHA, C22:6n3) or arachidonic acid (AA, C20:4n6) were included in the culture medium in concentrations of 15 µmol/L using ethanol as a vehicle (0.2 % v/v final ethanol concentration). Cells were cultured in the enriched media totaling 72 h. Stimulation of cells was performed in the last 24 h of fatty acid supplementation by addition of LTA (0.5 µg/mL; from Staphylococcus aureus).
2022-03-03 | GSE162994 | GEO
Project description:We report the transcriptome of murine macrophages (cell line: RAW264.7) after supplementation with polyunsaturated fatty acids (PUFA) and stimulation with LPS. The fatty acids docosahexaenoic acid (DHA, C22:6n3) or arachidonic acid (AA, C20:4n6) were included in the culture medium in concentrations of 15 µmol/L using ethanol as a vehicle (0.2 % v/v final ethanol concentration). Cells were cultured in the enriched media totaling 72 h. Stimulation of cells was performed in the last 24 h of fatty acid supplementation by addition of LPS (1 µg/mL; from E. coli serotype 0111:B4).
2022-03-03 | GSE142088 | GEO
Project description:This model is a supplementary material of publication
“Kinetic and stoichiometric modeling-based analysis of do-cosahexaenoic acid (DHA) production potential by C.cohnii from glycerol, glucose and ethanol”
by Kristaps Berzins, Reinis Muiznieks, Matiss R. Baumanis, Inese Strazdina, Karlis Shvirksts, Santa Prikule, Vytautas Galvanauskas, Daniel Pleissner, Agris Pentjuss, Mara Grube, Uldis Kalnenieks and Egils Stalidzans
This is a kinetic model of Crypthecodinium cohnii central carbon metabolism during fatty acid synthesis. The model is aimed at cytosolic acetyl coenzyme-A production, which is the precursor of fatty acids.
The model contains 35 reactions and 36 species split into three compartments – extracellular, cytosol and mitochondria. It was assumed that dry weight accounts for 33% of wet weight and that 1ml = 1g. The mitochondria volume is 1% of cytosol volume. Both glucose and glycerol can be used as substrates in this model, however, the model was designed for single substrate use only. For use of ethanol as substrate, see MODEL2112290001 .
The model is preset for steady state calculation using glucose. To use glycerol as a substrate it is possible to change species concentrations manually or use the predefined parameter set.
The model contains 31 global quantities which were used to optimize the model during parameter estimation. These global quantities include amino acid concentrations for each enzyme, the total amino acid concentration used in enzymes, the sum transport reaction variable parameters and the total concentration of species.
All enzymatic reactions contain a parameter k, which can be used for change of enzyme expression levels in case of optimization of product flux or yield. Currently all the parameters k are set for 1, which corresponds to wild-type.
The model was made for steady-state. For glucose and glycerol a steady state resolution of 1e-6 can be used.
2022-05-06 | MODEL2112280001 | BioModels
Project description:We report the transcriptome of human endothelial cells (cell line: TIME) after supplementation with polyunsaturated fatty acids (PUFA) and/or stimulation with pro-inflammatory cytokines. The fatty acids docosahexaenoic acid (DHA, C22:6n3) or arachidonic acid (AA, C20:4n6) were included in the culture medium in concentrations of 15 µmol/L using ethanol as a vehicle (0.2 % v/v final ethanol concentration). Cells were cultured in the enriched media totaling 144 h. Stimulation of cells was performed in the last 24 h of fatty acid supplementation by addition of the cytokines IL-1β, TNF-α, and IFN-γ each in a concentration of 5 ng/ml.
2021-12-01 | GSE141957 | GEO
Project description:Thraustochytrids of the genera Schizochytrium and Aurantiochytrium accumulate oils rich in the essential, marine n3 fatty acid docosahexaenoic acid (DHA). DHA production in Aurantiochytrium sp T66 was studied with the aim to provide more knowledge about factors that affect the DHA-productivities and the contributions of the two enzyme systems used for fatty acid synthesis in thraustochytrids, fatty acid synthetase (FAS) and PUFA-synthase. Fermentations with nitrogen starvation, which is well-known to initiate lipid accumulation in oleaginous organisms, were compared to fermentations with nitrogen in excess where lipid accumulation was obtained by oxygen limitation. The specific productivities of fatty acids originating from FAS were considerably higher under nitrogen starvation than with nitrogen in excess, while the specific productivities of DHA were the same at both conditions. Global transcriptome analysis showed significant up-regulation of FAS under N-deficient conditions, while the PUFA-synthase genes were only marginally upregulated. Neither of them was upregulated under O2-limitation where nitrogen was in excess, suggesting that N-starvation mainly affects the FAS and may be less important for the PUFA-synthase. The transcriptome analysis also revealed responses likely to be related to the generation of reducing power (NADPH) for fatty acid synthesis.
2019-12-19 | GSE134374 | GEO
Project description:Long-chain n-3 polyunsaturated fatty acids (n-3 LC-PUFAs) are collectively recognized triglyceride-lowering agents, and their preventive action is likely mediated by changes in gene expression. However, as most studies employ fish oil, which contains a mixture of n-3 LC-PUFAs, the docosahexaenoic acid (DHA)-specific transcriptional effects on lipid metabolism are still unclear. The aim of the present study was to further elucidate the DHA-induced transcriptional effects on lipid metabolism in the liver, and to investigate the effects of co-administration with other bioactive compounds having effects on lipid metabolism. To this purpose, HepG2 cells were treated for 6 or 24 h with DHA, the short-chain fatty acid propionate (PRO), and protocatechuic acid (PCA), the main human metabolite of cyanidin-glucosides. Following supplementation, we mapped the global transcriptional changes. PRO and PCA alone had a very slight effect on the transcriptome; on the contrary, supplementation of DHA highly repressed the steroid and fatty acid biosynthesis pathways, this transcriptional modulation being not affected by co-supplementation. Our results confirm that DHA effect on lipid metabolism are mediated at least in part by modulation of the expression of specific genes. PRO and PCA could contribute to counteracting dyslipidemia through other mechanisms.
2020-09-30 | GSE147718 | GEO
Project description:The present study aimed to determine the impact of dietary docosahexaenoic acid (DHA) on the metabolism of Atlantic salmon (Salmo salar). The effects of diets containing increasing levels of DHA (1 g kg-1, 5 g kg-1, 10 g kg-1, 15 g kg-1 and 20 g kg-1) on the liver transcriptome of post-smolt salmon was determined using regression analysis to elucidate patterns of gene expression and responses of specific metabolic pathways. Total RNA was isolated from liver of individual fish and analyzed using a custom 44K Atlantic salmon oligo-microarray. The expression of up to 911 unique annotated genes was significantly affected by dietary DHA inclusion relative to a low DHA reference diet. Using regression analysis, 797 unique genes were found with a significant linear correlation between expression level and dietary DHA. Gene-Set Enrichment Analysis (GSEA) identified a range of pathways that were significantly affected by dietary DHA content. Pathways that showed a significant response to dietary DHA level included those for long-chain polyunsaturated fatty acid biosynthesis, fatty acid elongation, steroid biosynthesis, glycan biosynthesis, protein export and protein processing in the endoplasmic reticulum. These findings suggest that in addition to clear roles in influencing lipid metabolic pathways, DHA also has key functional roles in other biosynthetic pathways distinct from lipid metabolism.
2015-08-20 | E-MTAB-3180 | biostudies-arrayexpress
Project description:Fatty acid synthesis is closely linked to nutrient availability and cellular energetic status. The committed step in fatty acid synthesis is the acetyl CoA carboxylase. Eukaryotes have two genes encoding acetyl CoA carboxylases, one encoding a cytosolic enzyme and another coding for a mitochondrial enzyme. They catalyze the synthesis of malonyl CoA in the cytosol and the mitochondria, respectively. While cytosolic malonyl CoA is the precursor for fatty acid synthesis, mitochondrial malonyl CoA controls the transfer of fatty acyl group into the mitochondria by inhibiting carnitine/palmitoyl transferase activity and thus, regulates β-oxidation. In Saccharomyces cerevisiae, β-oxidation is restricted to the peroxisomes, raising the question of the function of the mitochondrial isoform (HFA1). In this study, we replaced the cytosolic Acc1 with Hfa1 expressed in the cytosol by removing the mitochondrial leader peptide, under control of the HFA1 promoter. We studied fatty acid synthesis and transcription profiles in this strain during starvation for carbon or nitrogen, using glucose or ethanol as the carbon source. Under all the conditions studied, the key sensor of energetic status, Snf1, was activated, indicating active inhibition of fatty acid synthesis. The pool size of fatty acids was smaller when Acc1 was replaced with truncated Hfa1 for fatty acid synthesis. Yet, the transcription profiles were similar in both the cases. These results point towards the conclusion that Hfa1 is either catalytically less efficient or it is more sensitive to inhibition by Snf1. Gene expression from a strain of Saccharomyces cerevisiae where cytosolic fatty acid synthesis occurs by mitochondrial acetyl CoA carboxylase (without its mitochondrial leader peptide) is compared with that in a reference strain while growing in chemostats on carbon or nitrogen starvation using glucose or ethanol as the carbon source. There are two strains (reference or mutant), two carbon sources (glucose or ethanol) and two limitations (carbon or nitrogen), resulting in 8 comparisons. Each array was performed in duplicate, resulting in 16 CEL files. Growth was limited by either carbon or nitrogen. When carbon was the limited nutrient, we tested growth on either glucose or ethanol (both using ammonium sulfate as the nitrogen source). When ammonium sulfate was limiting, we used either glucose or ethanol as the carbon source.
2010-06-08 | E-GEOD-21988 | biostudies-arrayexpress