Bulk RNA-seq analysis of the effects of ECHS1 knockdown on cardiomyocyte transcriptome
Ontology highlight
ABSTRACT:
ORGANISM(S): Rattus norvegicus
PROVIDER: GSE159039 | GEO | 2021/11/20
REPOSITORIES: GEO
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Project description:Short chain enoyl-CoA hydratase 1 (ECHS1) is involved in the second step of mitochondrial fatty acid β-oxidation (FAO), catalysing the hydration of short chain enoyl-CoA esters to short chain 3-hyroxyl-CoA esters. Genetic deficiency in ECHS1 (ECHS1D) is associated with a specific subset of Leigh Syndrome, a disease typically caused by defects in oxidative phosphorylation (OXPHOS). Here, we examined the molecular pathogenesis of ECHS1D using a CRISPR/Cas9 edited human cell ‘knockout’ model and fibroblasts from ECHS1D patients. Transcriptome analysis of ECHS1 ‘knockout’ cells showed reductions in key mitochondrial pathways, including the TCA cycle, receptor mediated mitophagy and nucleotide biosynthesis. Subsequent proteomic analyses confirmed these reductions and revealed additional defects in mitochondrial oxidoreductase activity and fatty acid β-oxidation. Functional analysis of ECHS1 ‘knockout’ cells showed reduced mitochondrial oxygen consumption rates when metabolising glucose or OXPHOS complex I-linked substrates, as well as decreased complex I and complex IV enzyme activities. ECHS1 ‘knockout’ cells also exhibited decreased OXPHOS protein complex steady-state levels (complex I, complex III2, complex IV, complex V and supercomplexes CIII2/CIV and CI/CIII2/CIV). Patient fibroblasts exhibit varied reduction of mature OXPHOS complex steady-state levels, with defects detected in CIII2, CIV, CV and the CI/CIII2/CIV supercomplex. Overall, these findings highlight the contribution of defective OXPHOS function, in particular complex I deficiency, to the molecular pathogenesis of ECHS1D.
2022-04-10 | GSE200252 | GEO
Project description:Short chain enoyl-CoA hydratase 1 (ECHS1) is involved in the second step of mitochondrial fatty acid β-oxidation (FAO), catalysing the hydration of short chain enoyl-CoA esters to short chain 3-hyroxyl-CoA esters. Genetic deficiency in ECHS1 (ECHS1D) is associated with a specific subset of Leigh Syndrome, a disease typically caused by defects in oxidative phosphorylation (OXPHOS). Here, we examined the molecular pathogenesis of ECHS1D using a CRISPR/Cas9 edited human cell ‘knockout’ model and fibroblasts from ECHS1D patients. Transcriptome analysis of ECHS1 ‘knockout’ cells showed reductions in key mitochondrial pathways, including the TCA cycle, receptor mediated mitophagy and nucleotide biosynthesis. Subsequent proteomic analyses confirmed these reductions and revealed additional defects in mitochondrial oxidoreductase activity and fatty acid β-oxidation. Functional analysis of ECHS1 ‘knockout’ cells showed reduced mitochondrial oxygen consumption rates when metabolising glucose or OXPHOS complex I-linked substrates, as well as decreased complex I and complex IV enzyme activities. ECHS1 ‘knockout’ cells also exhibited decreased OXPHOS protein complex steady-state levels (complex I, complex III2, complex IV, complex V and supercomplexes CIII2/CIV and CI/CIII2/CIV). Patient fibroblasts exhibit varied reduction of mature OXPHOS complex steady-state levels, with defects detected in CIII2, CIV, CV and the CI/CIII2/CIV supercomplex. Overall, these findings highlight the contribution of defective OXPHOS function, in particular complex I deficiency, to the molecular pathogenesis of ECHS1D.
2023-05-10 | PXD032761 | Pride
Project description:Pseudomonas putida KT2440 is a well-known model organism for the medium chain length (mcl) PHA accumulation. (R)-Specific enoyl-coenzyme A hydratase (PhaJ) was considered to be the main supplier of monomers for PHA synthesis by converting the -oxidation intermediate, trans-2-enoyl-CoA to (R)-3-hydroxyacyl-CoA when fatty acids (FA) are used. Three PhaJ homologues, PhaJ1, PhaJ4 and MaoC are annotated in P. putida KT2440. To investigate the relationship of fatty acids - PHA metabolism and the role of each PhaJ in PHA biosynthesis in P. putida KT2440, a series of P. putida KT2440 knockouts was obtained. PHA content and monomer composition in WT and mutants under different growth conditions were analysed. However, when all three PhaJ homologues were deleted, the mutant still accumulated PHA up to 10.7 % of the cell dry weight (CDW). To identify other potential PHA monomer suppliers by analysing the proteome of the phaJ1maoCphaJ4. The proteomes of the WT, phaJ1phaJ4 and phaJ1maoCphaJ4 strains in MSM medium with octanoate under nitrogen limited condition were detected. In addition, we found that the deletion of PhaJ1 in P. putida KT2440 has a negative impact on the PHA accumulation in cells cultivated on glucose with nitrogen limitation conditions. It seems PhaJ1 also mediates the synthesis of PHA when glucose was used as the carbon and energy source. To investigate the role of PhaJ1 in PHA accumulation with glucose, the proteomes of P. putida KT2440 wild type, phaJ1, phaJ1phaJ4 and phaJ1maoCphaJ4 mutant growing on glucose were detected and compared.
2023-05-10 | PXD037932 | Pride
Project description:Loss of Mitochondrial Fatty Acid Beta-Oxidation Protein Short Chain Enoyl-CoA Hydratase Disrupts Oxidative Phosphorylation Protein Complex Stability and Function
| PRJNA823744 | ENA
Project description:Pseudomonas putida KT2440 is a well-known model organism for the medium chain length (mcl) PHA accumulation. (R)-Specific enoyl-coenzyme A hydratase (PhaJ) was considered to be the main supplier of monomers for PHA synthesis by converting the -oxidation intermediate, trans-2-enoyl-CoA to (R)-3-hydroxyacyl-CoA when fatty acids (FA) are used. Three PhaJ homologues, PhaJ1, PhaJ4 and MaoC are annotated in P. putida KT2440. To investigate the relationship of fatty acids - PHA metabolism and the role of each PhaJ in PHA biosynthesis in P. putida KT2440, a series of P. putida KT2440 knockouts was obtained. PHA content and monomer composition in WT and mutants under different growth conditions were analysed. However, when all three PhaJ homologues were deleted, the mutant still accumulated PHA up to 10.7 % of the cell dry weight (CDW). To identify other potential PHA monomer suppliers by analysing the proteome of the phaJ1maoCphaJ4. The deletion of (R)-3-hydroxydecanoyl-ACP:CoA transacylase (PhaG), which connects de novo FA and PHA synthesis pathways, while causing further 1.8-fold decrease in PHA content, did not abolish PHA accumulation. Further proteome analysis revealed quinoprotein alcohol dehydrogeanses PedE and PedH as potential monomer suppliers, but when these were deleted PHA level remained at 2.2 – 14.8 % CDW depending on the fatty acid used, and whether nitrogen limitation was applied. To identify the other non-specific dehydrogenases supply monomers for PHA synthesis, we analysed the proteome of the sextuple mutant under nitrogen limiting and non-limiting conditions.
2023-05-10 | PXD037937 | Pride
Project description:Acquired deficiency of the peroxisomal bi-functional enzyme enoyl-CoA hydratase/3-hydroxyacyl CoA dehydrogenase is a metabolic vulnerability in murine hepatoblastoma
| PRJNA658322 | ENA
Project description:Lysine crotonylation (Kcr) is a recently-identified protein short-chain acylation. We have previously reported that chromodomain Y-like transcription corepressor CDYL acts as a crotonyl-CoA hydratase and negatively regulates histone Kcr. However, the global crotonylome of CDYL-regulated Kcr on non-histone substrates remains unclear. Using proteome-wide quantitative Kcr analysis, we identified 14,311 Kcr sites across 3,734 proteins in HeLa cells, providing by far the largest crotonylome data set from a single study. Upon depletion of CDYL, 1,141 Kcr sites from 759 proteins were increased by more than 1.5 fold, and 933 Kcr sites from 528 proteins were decreased by more than 0.67 fold. Upregulated crotonylome alterations upon CDYL depletion include components from diverse cellular pathways such as RNA splicing, DNA replication, and amino acid metabolism. Specifically, CDYL regulates K88 and K379 of crotonylation on RPA1, which affects its binding to other DNA repair factors including BLM, DNA2L, RAD50 and WRN. We showed evidence that CDYL-mediated RPA1 crotonylation is critical for the homologous recombination (HR) repair of camptothecin (CPT)-induced DNA damage. Together, our results provide a broad lysine crotonylome in response to CDYL and shed new light on the role of RPA1 Kcr in DNA repair, implicating functional importance of Kcr on non-histone substrates in diverse cellular processes.
2020-04-02 | PXD013616 | Pride
Project description:In this study we report that histone crotonylation promotes human embryonic stem cell differentiation to endoderm cells. Addition of crotonate, a precursor for crotonyl-CoA and therefore histone crotonylation, dramatically enhanced endoderm cell differentiation from human embryonic stem cells, while incubation of acetate, a precursor of acetyl-CoA and therefore histone acetylation, did not change the efficiency of endoderm differentiation.
2021-02-23 | GSE130341 | GEO
Project description:Disruption of peripheral circadian rhyme pathways dominantly leads to metabolic disorders. Studies on circadian rhythm proteins in the heart indicated a role for Clock or Per2 in cardiac metabolism. In fact, Per2-/- mice have larger infarct sizes with a deficient lactate production during myocardial ischemia. To test the hypothesis that cardiac Per2 represents an important regulator of cardiac metabolism during myocardial ischemia, we performed lactate measurements during reperfusion in Per1-/-, Per2-/- or wildtype mice followed by gene array studies using various ischemia-reperfusion protocols comparing wildtype and Per2-/- mice. Lactate measurements in whole blood confirmed a dominant role of Per2 for lactate production during myocardial ischemia. Surprisingly, high-throughput gene array analysis of eight different conditions on one 24-microarray plate revealed dominantly lipid metabolism as differentially regulated pathway in wildtype mice when compared to Per2-/-. In all treatment groups, the enzyme enoyl-CoA hydratase, which is essential in fatty acid beta-oxidation, was regulated in wildtype animals only. Studies using nuclear magnet resonance imaging (NMRI) confirmed altered fatty acid populations with higher mono-unsaturated fatty acid levels in hearts from Per2-/- mice. Unexpectedly, studies on gene regulation during reperfusion revealed solely pro inflammatory genes as differentially regulated 'Per2-genes'. Subsequent studies on inflammatory markers showed increasing IL6 or TNFa levels during reperfusion in Per2-/- mice. In summary, these studies reveal a novel role of cardiac Per2 for fatty acid metabolism or inflammation during myocardial ischemia and reperfusion.
2013-08-21 | GSE45818 | GEO
Project description:Lysine acylations, such as acetylation, succinylation, or glutarylation, are post-translational modifications that regulate protein function. In mitochondria, lysine acylation is predominantly non-enzymatic and only a specific subset of the proteome has been identified as acylated. Coenzyme A (CoA), a metabolite required in several metabolic pathways, can act as an acyl group carrier via a thioester bond. However, what controls the acylation of lysine residues in the mitochondria remains poorly understood. Using published datasets, we found that proteins with a CoA-binding site are more likely to be acetylated, succinylated, and glutarylated. Using computational modeling, we discovered that, in CoA-binding proteins, lysine residues near the CoA-binding pocket are more likely to be acylated than those far away from the CoA-binding pocket. We hypothesized that acyl-CoA binding enhances the acylation of nearby lysine residues. To experimentally test this hypothesis, we used enoyl-CoA hydratase short chain 1 (ECHS1), a mitochondrial protein with a CoA-binding pocket, and co-incubated ECHS1 with succinyl-CoA and CoA. Using mass spectrometry, we found that succinyl-CoA induced widespread lysine succinylation and that CoA competitively inhibited ECHS1 succinylation. In addition, CoA-induced inhibition at a particular lysine site was inversely correlated with the distance between this lysine residue and the CoA-binding pocket. This indicated that CoA acts as a competitive inhibitor of ECHS1 succinylation by binding to the CoA-binding pocket. Together, this study suggests proximal acylation at protein CoA-binding sites is a primary mechanism for lysine acylation in the mitochondria.
2022-05-09 | MSV000089448 | MassIVE