Similar Datasets
Project description:ProVitamin A and Vitamin E biosynthesis in Zea mays.
2012-09-17 | E-MTAB-4290 | biostudies-arrayexpress
Project description:Vitamin D deficiency poses a major global health challenge, shaped by environmental and genetic determinants. In this genetic context, the recently discovered rs11542462 nonsense variant in the short-chain dehydrogenase/reductase 42E1 (SDR42E1) gene emerges as a critical regulator, though its biological implications remain largely unexplored. Our comprehensive bioinformatic assessments revealed pronounced expression of SDR42E1 in skin keratinocytes and the analogous HaCat human keratinocyte cell lines, prompting us to select the latter as an experimental model. Employing CRISPR/Cas9 technology and an integrated multi-omics approach, combining transcriptomics and proteomics, we explored SDR42E1's functions, focusing on its localization, role in lipid and steroid biosynthesis, and the consequent effects on vitamin D biosynthesis. We highlighted the significant cytoplasmic presence of the SDR42E1 protein, essential for lipid and steroid production. Our whole transcriptomics analysis of the SDR42E1 depleted model showed a notable disruption in the steroid biosynthesis pathway by 1.6-fold (P = 0.03). This disruption was accompanied by considerable alterations in genes involved in vitamin D synthesis, a finding supported by our proteomics data. Notably, SERPINB2 (P = 2.17E−103), EBP (P = 2.46E−13), and DHCR7 (P = 8.03E−09) showed significant elevations by ~2-3 fold, while ALPP (P < 2.2E−308), SLC7A5 (P = 1.96E−215), and CYP26A1 (P = 1.06E−08) decreased by ~1.5-3 fold. These alterations led to an accumulation of 7-dehydrocholesterol, preventing its conversion to vitamin D3, as evidenced by our drug enrichment analysis (P = 4.39E−06). This investigation unveils SDR42E1's pivotal role in vitamin D homeostasis and its broader impact on metabolic pathways. Our findings provide a foundation for future research and highlight the potential of precision medicine in addressing vitamin D deficiency, offering significant insights into the genetic regulation of vitamin D biosynthesis.
2024-08-22 | GSE262704 | GEO
Project description:Vitamin C (ascorbic acid, AA), as essential micro-nutrient and antioxidant, can affect multiple cellular processes. Previously, we showed that Vitamin C supplement could promote the proliferation and suppress apoptosis of porcine Sertoli cells, via modulating the global nucleic acid methylation levels to alter transcriptome and proteomics. Due to the differences between pig and rodent species, here we investigated the effects of Vitamin C on mouse TM4 Sertoli cells. Vitamin C (250µM) treatment of mouse TM4 Sertoli cells for 36h could significantly increase cell viability, promote cell proliferation and decrease the cell percentage with early apoptosis. Vitamin C (250µM, 36h) also significantly decreased ROS level, elevated mitochondrial function, altered the levels of nucleic acid N6-methylation (m6A) and modified the levels of histone H3 trimethylation (H3K4me3, H3K9Me3 and H3K36me3) of mouse TM4 Sertoli cells. Vitamin C (250µM, 36h) promoted the secretion of anti-müllerian hormone and Estrodiol, but decreased lactate metabolite in mouse TM4 Sertoli cells. RNA-seq identified 112 differentially expressed genes (DEGs) (74 up- and 38 down-regulated) (P≤0.05, |log2Fold Change|≥1) as induced by Vitamin C in mouse TM4 Sertoli cells. Gene enrichment analysis found multiple significantly enriched biological terms or pathways, including GO terms of regulation of response to biotic stimulus, homeostasis of number of cells, positive regulation of tumor necrosis factor production, GTPase activity, calmodulin binding etc., and KEGG signal pathways of calcium signal pathway, cGMP-PKG signaling pathway, steroid biosynthesis, arginine biosynthesis etc. 9 DEGs were selected for RT-qPCR validation and 8 of them showed the change trend consistent to RNA-seq. Taken together, Vitamin C (250µM, 36h) could modulate the functions of mouse TM4 Sertoli cells, through modifying the transcriptome to affect multiple signal pathways.
2024-07-31 | GSE241623 | GEO
Project description:The l-galactose (Smirnoff-Wheeler) pathway represents the major route to l-ascorbic acid (vitamin C) biosynthesis in plants. Arabidopsis thaliana VTC2 and its paralogue VTC5 function as GDP-l-galactose phosphorylases converting GDP-l-galactose to l-galactose-1-P, thus catalyzing the first committed step in the biosynthesis of l-ascorbate. Here we report that the l-galactose pathway of ascorbate biosynthesis described in higher plants is conserved in green algae. The Chlamydomonas reinhardtii genome encodes all the enzymes required for vitamin C biosynthesis via the Smirnoff-Wheeler pathway. We have characterized recombinant C. reinhardtii VTC2 as an active GDP-l-galactose phosphorylase. C. reinhardtii cells exposed to oxidative stress show increased VTC2 mRNA and l-ascorbate levels. We have also shown that enzymatic components of the ascorbate-glutathione system (e.g. ascorbate peroxidase, Mn superoxide dismutase, dehydroascorbate reductase) are up-regulated in response to increased oxidative stress. These results indicate that C. reinhardtii VTC2, like its plant homologs, is a key enzyme in ascorbate biosynthesis in green algae and together with components of the ascorbate recycling system represents the major route in providing protective levels of ascorbate in oxidatively stressed algal cells. Our results suggest that C. reinhardtii cells exposed to oxidative stress conditions produce more ascorbate both by de novo synthesis (Smirnoff-Wheeler pathway) and by recycling via the ascorbate-glutathione cycle. Sampling of Chlamydomonas 2137 exposed to hydrogen peroxide
2012-05-02 | E-GEOD-34826 | biostudies-arrayexpress
Project description:Lactobacillus reuteri has been shown to encode a vitamin B12 biosynthesis pathway that is phylogenetically related to the one present in some representatives of gamma-proteobacteria such as Salmonella and Yersinia. Here we present evidence supporting that the similarities between these otherwise unrelated organisms extend to their regulatory mechanisms. Keywords: cell type comparison Loop design
2010-05-17 | E-GEOD-13289 | biostudies-arrayexpress
Project description:The l-galactose (Smirnoff-Wheeler) pathway represents the major route to l-ascorbic acid (vitamin C) biosynthesis in plants. Arabidopsis thaliana VTC2 and its paralogue VTC5 function as GDP-l-galactose phosphorylases converting GDP-l-galactose to l-galactose-1-P, thus catalyzing the first committed step in the biosynthesis of l-ascorbate. Here we report that the l-galactose pathway of ascorbate biosynthesis described in higher plants is conserved in green algae. The Chlamydomonas reinhardtii genome encodes all the enzymes required for vitamin C biosynthesis via the Smirnoff-Wheeler pathway. We have characterized recombinant C. reinhardtii VTC2 as an active GDP-l-galactose phosphorylase. C. reinhardtii cells exposed to oxidative stress show increased VTC2 mRNA and l-ascorbate levels. We have also shown that enzymatic components of the ascorbate-glutathione system (e.g. ascorbate peroxidase, Mn superoxide dismutase, dehydroascorbate reductase) are up-regulated in response to increased oxidative stress. These results indicate that C. reinhardtii VTC2, like its plant homologs, is a key enzyme in ascorbate biosynthesis in green algae and together with components of the ascorbate recycling system represents the major route in providing protective levels of ascorbate in oxidatively stressed algal cells. Our results suggest that C. reinhardtii cells exposed to oxidative stress conditions produce more ascorbate both by de novo synthesis (Smirnoff-Wheeler pathway) and by recycling via the ascorbate-glutathione cycle.
2012-05-03 | GSE34826 | GEO
Project description:Lactobacillus reuteri has been shown to encode a vitamin B12 biosynthesis pathway that is phylogenetically related to the one present in some representatives of gamma-proteobacteria such as Salmonella and Yersinia. Here we present evidence supporting that the similarities between these otherwise unrelated organisms extend to their regulatory mechanisms. Keywords: cell type comparison
2008-10-31 | GSE13289 | GEO
Project description:Shotgun sequencing of the gut microbiome to look at vitamin K biosynthesis
| PRJNA347511 | ENA
Project description:Kidneys from our transgenic mouse model of early stage cancer of the kidney (TRACK) exhibit a mitochondrial stress response (MSR) signature, as indicated by increased mRNA for Atf4, a key transcription factor activated in the MSR, and increased transcripts of Atf4 targets, including Asns, Mthfd2, Trib3, Ddit3(Chop;Gadd153), Atf3, Ppp1r15a(Gadd34), Aldh1l2, Fgf21, and Slc20a1. By performing transcriptomics analyses from TRACK versus wild type (WT) kidneys after dietary vitamin A deprivation, we show that both vitamin A deficiency (VAD) and expression of constitutively active HIF1α intensify the MSR, redirect amino acids to one carbon metabolism, and facilitate the biosynthesis of reduced glutathione.
2020-08-01 | GSE134933 | GEO
Project description:Tuberculosis is a global health threat that affects millions of people every year, and treatment-limiting toxicity remains a considerable source of treatment failure. Recent reports have characterized the nature of hPXR-mediated hepatotoxicity and systemic toxicity of antitubercular drugs. The antitubercular drug isoniazid plays a role in such pathologic states as acute intermittent porphyria, anemia, hepatotoxicity, hypercoagulable states (deep vein thrombosis, pulmonary embolism, or ischemic stroke), pellagra (vitamin B3 deficiency), peripheral neuropathy, and vitamin B6 deficiency. However, the mechanisms by which isoniazid administration leads to these states are unclear. To elucidate the mechanism of rifampicin- and isoniazid-induced liver and systemic injury, we performed tandem mass tag mass spectrometry-based proteomic screening of mPxr–/– and hPXR mice treated with combinations of rifampicin and isoniazid. Proteomic profiling analysis suggested that the hPXR liver proteome is affected by antitubercular therapy to disrupt [Fe–S] cluster assembly machinery, [2Fe–2S] cluster-containing proteins, CYP450 enzymes, heme biosynthesis, homocysteine catabolism, oxidative stress responses, vitamin B3 metabolism, and vitamin B6 metabolism. These findings provide insight into the etiology of some of these processes and potential targets for subsequent investigations.
2020-07-19 | PXD019505 | Pride