Ontology highlight
ABSTRACT:
PROVIDER: PRJNA533471 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8924910.fastq.gz | Fastqsanger.gz | |||
| SRR8924920.fastq.gz | Fastqsanger.gz | |||
| SRR8924930.fastq.gz | Fastqsanger.gz | |||
| SRR8924911.fastq.gz | Fastqsanger.gz | |||
| SRR8924921.fastq.gz | Fastqsanger.gz |
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Project description:In this experiment we performed the transcriptional profiling of the wild type yeast Saccharomyces cerevisiae upon treatment with lovastatin or zaragozic acid. These drugs are known to exert a repressing effect on the sterol branch of the isoprenoid pathway, but their action differs at the level of FPP biosynthesis. While lovastatin decreases FPP availability because it is an inhibitor of HMGR, zaragozic acid increases this level because it inhibits squalene synthase. In this work, we were interested especially in genes, whose expression would be oppositely regulated in the presence of lovastatin or zaragozic acid, since these genes could be affected by variation in FPP level and thus related somehow to the isoprenoid pathway.
2009-09-01 | GSE12984 | GEO
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.
2018-11-28 | MSV000083169 | MassIVE
Project description:Plasmodium falciparum is the etiological agent of human malaria, one of the most widespread diseases in tropical and subtropical world regions. One of the biggest problems in controlling the disease is the emergence of drug resistance, which leads to the need to discover new antimalarial compounds. One of the most promissory drugs purposed is fosmidomycin, an inhibitor of the biosynthesis of isoprene units by the methylerythritol 4-phosphate (MEP) pathway which in some cases failed in clinic studies. Once formed, isoprene units are condensed to form longer structures such as farnesyl and geranylgeranyl pyrophosphate (GGPP), which are necessary for heme O and A formation, ubiquinone, and dolichyl phosphate biosynthesis as well as for protein isoprenylation. Even though the natural substrates of polyprenyl transferases and syntheses are polyprenyl pyrophosphates, it was already demonstrated that isoprenoid alcohols (polyprenols) such as farnesol (FOH) and geranylgeraniol (GGOH) can rescue parasites from fosmidomycin. This study better investigated how this rescue phenomenon occurs by performing drug-rescue assays. By this, it was observed that phytol (POH), a 20-carbon plant isoprenoid, rescues parasites from the fosmidomycin effect, similarly to FOH or GGOH. Contrarily, neither dolichols nor nonaprenol rescue parasites from fosmidomycin. Considering this, here we characterized the transport of FOH, GGOH, and POH. Once incorporated, it was observed that these substances are phosphorylated, condensed into longer isoprenoid alcohols, and incorporated into proteins and dolichyl phosphates. Through proteomic and radiolabelling approaches, it was found that prenylated proteins are naturally attached to several isoprenoids including GGOH, dolichol, and POH if exogenously added. Furthermore, results suggest the presence of at least two promiscuous protein prenyltransferases in the parasite: one enzyme which can use FPP among other unidentified substrates and another enzyme that can use GGOH, POH, and dolichols among other substrates not identified here. Thus, was obtained further evidence for dolichols and other isoprenoid products attached to proteins. This study helps better understand apicoplast-targeting antimalarials mechanism of action as well as novel posttranslational modifications of proteins.
2022-11-28 | PXD036092 | Pride
Project description:Raw data files from native mass spectrometry analyses examining the interactions between methylerythritol phosphate (MEP) pathway metabolites and Escherichia coli K-12 fatty acid biosynthesis enzymes. Recorded in positive mode direct injection.
2024-10-16 | MSV000096110 | GNPS
Project description:Isovaleryl-CoA (IV-CoA) is usually derived from the degradation of leucine using the Bkd (branched-chain ketoacid dehydrogenase) complex. In myxobacteria we have previously identified an alternative pathway for IV-CoA formation that branches from the well-known mevalonate dependent isoprenoid biosynthesis pathway and we could already identify the 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) synthase (MvaS) to be involved in this pathway in Myxococcus xanthus which is induced under leucine limiting conditions like in mutants impaired in leucine degradation or during myxobacterial fruiting body formation. Here we show that proteins involved in leucine degradation are also involved in the alternative IV-CoA biosynthesis by catalyzing the reverse reactions of that used in leucine degradation. Moreover, we conducted a global gene expression experiment comparing vegetative cells of wild type and a bkd mutant. Thus we could identify a five-gene operon which was highly upregulated in a bkd mutant and that contains the mvaS gene and other genes which might be involved in a mevalonate-shunt pathway leading from mevalonate to 3-methylglutaconyl-CoA. Additionally, several genes involved in outer membrane biosynthesis and a plethora of genes encoding regulatory proteins are decreased explaining the complex phenotype of a bkd mutant that includes a lack of adhesion in developmental submers culture. 6 independent biological replicates. Normalized ratios to Cy3.
2008-05-01 | E-GEOD-10818 | biostudies-arrayexpress
Project description:Gram-negative bacteria in the order Rickettsiales are obligate intracellular parasites that cause human diseases such typhus and spotted fever. They have evolved a dependence on essential nutrients and metabolites from the host cell as a consequence of extensive genome streamlining. However, it remains largely unknown which nutrients they require and whether their metabolic dependency can be exploited therapeutically. Here, we describe a genetic rewiring of bacterial isoprenoid biosynthetic pathways in the Rickettsiales that has resulted from reductive genome evolution. We further investigated whether the spotted fever group Rickettsia species Rickettsia parkeri scavenges isoprenoid precursors directly from the host. Using targeted mass spectrometry in uninfected and infected cells, we found decreases in host isoprenoid products and concomitant increases in bacterial isoprenoid metabolites. Additionally, we report that bacterial growth is prohibited by inhibition of the host isoprenoid pathway with the statins class of drugs. We show that growth inhibition correlates with changes in bacterial size and shape that mimic those caused by antibiotics that inhibit peptidoglycan biosynthesis, suggesting statins inhibit cell wall synthesis. Altogether, our results describe an Achilles' heel of obligate intracellular pathogens that can be exploited with host-targeted therapeutics that interfere with metabolic pathways required for bacterial growth.
2019-10-31 | MTBLS846 | MetaboLights
Project description:Here we present the proteomic profile of mutant plants designated as eds16 (enhanced disease susceptibility), ceh1 (constitutively expressing HPL) as well as the ceh1 eds16 double mutant. CEH1 encodes 1-hydroxy-2-methyl-2-butenyl 4-diphosphate synthase (HDS), the enzyme controlling the bottleneck step of the biosynthesis of isopentenyl diphosphate via the 2-C-methyl-d-erythritol-4-phosphate (MEP) pathway in the plastids. Mutation of this enzyme in ceh1 mutant led to accumulation of high levels of the stress specific signaling metabolite 2c-methyl-D-erythritol 2,4-cylclodiphosphate (MEcPP), and consequently constitutive activation of a selected otherwise stress responsive genes. This data identifies the ensemble of stress responsive genes whose expression is regulated by the MEcPP signaling cascade.
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