Ontology highlight
ABSTRACT:
PROVIDER: PRJNA594463 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10613607_1.fastq.gz | Fastqsanger.gz | |||
| SRR10613607_2.fastq.gz | Fastqsanger.gz | |||
| SRR10613608.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.
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Project description:The statins are a family of inhibitors of the 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase enzyme, which converts acetyl-CoA into mevalonic acid. Since HMG-CoA reductase catalyzes the rate-limiting step in the mevalonate pathway of cholesterol biosynthesis, it was thought that the major clinical benefit of statins was to reduce cholesterol levels in the bloodstream; statins are thus in wide clinical use for the prevention and treatment of cardiovascular disease. Nonetheless, mevalonate is also the precursor of isoprenoid compounds, which are substrates for the post-translational modification of many proteins involved in cell signaling. The blockade of isoprenoid synthesis might explain the pleiotropic effects described for statins in extrahepatic tissues, including inhibition of pathogen infection and anti-inflammatory and immunomodulatory activities. We used microarrays to find differentially expressed genes in spontaneous breast tumors from mice treated with lovastatin (Lov) or vehicle (ethanol) as control.
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Project description:The statins are a family of inhibitors of the 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase enzyme, which converts acetyl-CoA into mevalonic acid. Since HMG-CoA reductase catalyzes the rate-limiting step in the mevalonate pathway of cholesterol biosynthesis, it was thought that the major clinical benefit of statins was to reduce cholesterol levels in the bloodstream; statins are thus in wide clinical use for the prevention and treatment of cardiovascular disease. Nonetheless, mevalonate is also the precursor of isoprenoid compounds, which are substrates for the post-translational modification of many proteins involved in cell signaling. The blockade of isoprenoid synthesis might explain the pleiotropic effects described for statins in extrahepatic tissues, including inhibition of pathogen infection and anti-inflammatory and immunomodulatory activities. We used microarrays to find differentially expressed genes in spontaneous breast tumors from mice treated with lovastatin (Lov) or vehicle (ethanol) as control. Standard single channel experimental design with biological replicates: gene expression signals from 5 treated tumor samples were compared to 5 non-treated tumor samples using Affymetrix GeneChips (MG430 v2.0).
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Project description:Carotenoids are essential natural compounds for human nutrition and play key roles in plants as photosynthetic pigments and as precursors of hormones and apocarotenoids. Tomato is a major model for carotenoid metabolism, where genetic variation strongly influences carotenoid composition during fruit ripening. Here we present an extensive biochemical and molecular characterization of five tomato carotenoid mutants—apricot (at), yellow flesh (r), tangerine (t), Delta (Del) and Beta (B)—across three ripening stages (mature green, breaker and red ripe). Gene-expression profiling (Affymetrix microarrays) was integrated with targeted isoprenoid metabolomics (carotenoids, chlorophylls, tocochromanols, quinones and ABA) and correlation-based analyses. Isoprenoid profiles showed strong, stage-dependent remodeling that extended beyond expected substrate/product changes and was accompanied by substantial transcriptional variation, often independent of the position of the mutated step in the pathway. The integrated analysis highlighted regulatory links between transcripts and metabolites and pointed to lycopene cyclization as a central node in isoprenoid network rewiring during ripening, improving our understanding of mechanisms controlling isoprenoid accumulation in tomato fruit. Carotenoids are key bioactive compounds, and tomato is a major model to study how genetic variation shapes their accumulation during fruit ripening. We profiled five tomato carotenoid mutants (apricot at, yellow flesh r, tangerine t, Delta Del, Beta B) across three ripening stages using Affymetrix gene-expression arrays integrated with targeted isoprenoid metabolomics (carotenoids, chlorophylls, tocochromanols, quinones, ABA) and correlation analyses. The data reveal strong stage-dependent remodeling and highlight lycopene cyclization as a central hub in isoprenoid pathway rewiring during ripening.
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