Ontology highlight
ABSTRACT:
PROVIDER: PRJNA979011 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR24806556.fastq.gz | Fastqsanger.gz | |||
| SRR24806557.fastq.gz | Fastqsanger.gz | |||
| SRR24806558.fastq.gz | Fastqsanger.gz | |||
| SRR24806559.fastq.gz | Fastqsanger.gz | |||
| SRR24806560.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 6 |
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Project description:An alternative for utilization of D-xylose, the non-phosphorylative Weimberg pathway was established in M. thermophila. Changes in transcript levels were surveyed in mutants. Transcriptome analysis revealed that the D-xylose dehydrogenase gene was significantly upregulated after deletion of D-xylose reductase when cultured in D-xylose media. Besides, genes belong to ribosome, biosynthesis of amino acids, biosynthesis of cofactors and carbon metabolism involved in growth were enriched in strains containing Weimberg pathway.
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Project description:Microglia modulate their cell state in response to various stimuli. Changes to cellular lipids often accompany shifts in microglial cell state, but the functional significance of these metabolic changes remains poorly understood. In human induced pluripotent stem cell-derived microglia, we observed that both extrinsic activation (by lipopolysaccharide treatment) and intrinsic triggers (the Alzheimer’s disease-associated APOE4 genotype) result in accumulation of triglyceride-rich lipid droplets. We demonstrate that lipid droplet accumulation is not simply concomitant with changes in cell state. In fact, both triglyceride biosynthesis and catabolism are necessary for the activation-induced transcription and the secretion of inflammatory cytokines and chemokines as well as the changes in phagocytosis of many substrates including the amyloid-beta peptide. In microglia harboring the Alzheimer’s disease risk APOE4 genotype, inhibiting triglyceride biosynthesis modifies the transcription of immune response genes and attenuates disease-associated transcriptional states. In addition, this inhibition rescues microglial surveillance defects observed in slices from APOE4 humanized transgenic mice. Together, our findings establish that modulating triglyceride metabolism can be used to tune microglial immunometabolism in response to extrinsic activation and in APOE4-associated disease.
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Project description:Pantothenate is a key vitamin for the intracellular biosynthesis of the essential molecule coenzyme A (CoA). Pantothenate can be biosynthesised or is taken take up by cells via plasma membrane transporters. In the cell, pantothenate, ATP and cysteine are required to synthesise CoA via five enzymatic steps. This canonical CoA biosynthesis route is well-studied in various organisms. Alternative routes that begin with the uptake of pantetheine (PanSH) or 4′-phosphopantetheine (PPanSH) as initial CoA precursors also exist. These alternative routes are vital for numerous unicellular organisms and are of interest for treating human diseases caused by defects in the canonical CoA biosynthesis pathway. In contrast to the uptake mechanisms for pantothenate, the cellular uptake mechanisms for PanSH and/or PPanSH are unresolved. Through a combination of in vivo experiments, yeast genetics and the use of chemical traceable compounds, we uncovered a non-canonical CoA biosynthesis pathway. We demonstrate that extracellularly, PanSH and PPanSH form mixed disulphides with glutathione, followed by uptake via the oligopeptide transporter Opt1. Once PanSH or PPanSH are imported, they are converted into CoA. Via this route several proteins essential for the canonical pantothenate-cysteine-dependent CoA biosynthesis pathway become dispensable. Additionally, we show that yeast strains cultured on PanSH or PPanSH have a growth advantage under conditions of decreased cysteine biosynthesis. The identified non-canonical CoA biosynthesis route provides a framework to treat CoA-linked diseases and to manipulate the growth of pathogenic or beneficial organisms that grow on PanSH or PPanSH.
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Project description:In addition to being a vital component of proteins, phenylalanine is also a precursor of numerous aromatic primary and secondary metabolites with broad physiological functions. In plants phenylalanine is synthesized predominantly via the arogenate pathway in plastids. Here, we describe the structure, molecular players and subcellular localization of a microbial-like phenylpyruvate pathway for phenylalanine biosynthesis in plants. Using a reverse genetic approach and metabolic flux analysis, we provide evidence that the cytosolic chorismate mutase is responsible for directing carbon flux towards cytosolic phenylalanine production via the phenylpyruvate pathway. We also show that an alternative transcription start site of a known plastidial enzyme produces a functional cytosolic prephenate dehydratase that catalyzes the conversion of prephenate to phenylpyruvate, the intermediate step between chorismate mutase and phenylpyruvate aminotransferase. Thus, our results complete elucidation of phenylalanine biosynthesis via phenylpyruvate in plants, showing that this pathway splits from the known plastidial arogenate pathway at chorismate, instead of prephenate as previously thought, and the complete pathway is localized in the cytosol.
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