Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Operation of a TCA cycle subnetwork in the mammalian nucleus

ABSTRACT:

Nucleic acid and histone modifications critically depend on tricarboxylic acid (TCA) cycle for substrates and co-factors. Although a few TCA cycle enzymes have been reported in the nucleus, the corresponding pathways are considered to operate in mitochondria. Here, we show that a part of the TCA cycle is operational also in the nucleus. Using 13C-tracer analysis, we identified activity of glutamine-to-fumarate, citrate-to-succinate, and glutamine-to-aspartate routes in the nuclei of HeLa cells. Proximity labeling mass-spectrometry revealed a spatial vicinity of the involved enzymes with core nuclear proteins. We further show nuclear localization of aconitase 2 and 2-oxoglutarate dehydrogenase in mouse embryonic stem cells. Nuclear localization of the latter enzyme, which produces succinyl-CoA, changed from pluripotency to differentiated state with accompanying changes in the nuclear protein succinylation. Together, our results demonstrate operation of an extended metabolic pathway in the nucleus warranting a revision of the canonical view on metabolic compartmentalization.

INSTRUMENT(S): Gas Chromatography MS - positive

SUBMITTER: Eleni Kafkia

PROVIDER: MTBLS2235 | MetaboLights | 2022-06-15

REPOSITORIES: MetaboLights

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	MTBLS2235	Other
	FILES	Other
	a_MTBLS2235_GC-MS_positive__metabolite_profiling.txt	Txt
	files-all.json	Other
	i_Investigation.txt	Txt

Items per page:

1 - 5 of 7

Similar Datasets

Operation of a TCA cycle subnetwork in the mammalian nucleus_mass4tox

Project description:Nucleic acid and histone modifications critically depend on central metabolism for substrates and co-factors. Although a few enzymes related to the formation of these required metabolites have been reported in the nucleus, the corresponding metabolic pathways are considered to function elsewhere in the cell. Here we show that a substantial part of the mitochondrial tricarboxylic acid (TCA) cycle, the biosynthetic hub of epigenetic modification factors, is operational also in the nucleus. Using 13C-tracer analysis, we identified activity of glutamine-to-fumarate, citrate-to-succinate, and glutamine-to-aspartate routes in the nuclei of HeLa cells. Proximity labeling mass-spectrometry revealed a spatial vicinity of the involved enzymes with core nuclear proteins, supporting their nuclear location. We further show nuclear localization of aconitase 2 and 2-oxoglutarate dehydrogenase in mouse embryonic stem cells. Together, our results demonstrate operation of an extended metabolic pathway in the nucleus warranting a revision of the canonical view on metabolic compartmentalization and gene expression regulation.

2022-10-14 | PXD032238 | Pride

Operation of a TCA cycle subnetwork in the mammalian nucleus

Project description:Nucleic acid and histone modifications critically depend on central metabolism for substrates and co-factors. Although a few enzymes related to the formation of these metabolites have been reported in the nucleus, the corresponding metabolic pathways are considered to function elsewhere in the cell. Here we show that a substantial part of the mitochondrial tricarboxylic acid (TCA) cycle, the biosynthetic hub of epigenetic modification factors, is operational also in the nucleus. Using 13C-tracer analysis, we identified activity of glutamine-to-fumarate, citrate-to-succinate, and glutamine-to-aspartate routes in the nuclei of HeLa cells. Proximity labeling mass-spectrometry revealed a spatial vicinity of the involved enzymes with core nuclear proteins, supporting their nuclear location. We further show nuclear localization of aconitase 2 and 2-oxoglutarate dehydrogenase in mouse embryonic stem cells. Together, our results demonstrate operation of an extended metabolic pathway in the nucleus warranting a revision of the canonical view on metabolic compartmentalization and gene expression regulation.

2022-10-13 | PXD022608 | Pride

Operation of a TCA cycle subnetwork in the mammalian nucleus

2022-10-14 | PXD032918 | Pride

Itaconate mediates an immunometabolic crosstalk between osteoclasts and osteoblasts

Project description:In this report, we show that both glucose and glutamine are essential during OC differentiation, and both contribute to the maintenance of the TCA cycle. Early differentiation is associated with a broken TCA cycle, with IRG1 siphoning TCA intermediates for the production of itaconate, which accumulates extracellularly, stimulating the function of osteoblasts in vitro an in vivo and in vivo and is necessary to retain bone mass in mice.

2024-07-14 | GSE208359 | GEO

A non-canonical tricarboxylic acid cycle underlies cellular identity

Project description:The tricarboxylic acid (TCA) cycle is a central hub of cellular metabolism, oxidizing nutrients to generate reducing equivalents for energy production and critical metabolites for biosynthetic reactions. Despite the importance of the products of the TCA cycle for cell viability and proliferation, mammalian cells display diversity in TCA-cycle activity. How this diversity is achieved, and whether it is critical for establishing cell fate, remains poorly understood. Here we identify a non-canonical TCA cycle that is required for changes in cell state. Genetic co-essentiality mapping revealed a cluster of genes that is sufficient to compose a biochemical alternative to the canonical TCA cycle, wherein mitochondrially derived citrate exported to the cytoplasm is metabolized by ATP citrate lyase, ultimately regenerating mitochondrial oxaloacetate to complete this non-canonical TCA cycle. Manipulating the expression of ATP citrate lyase or the canonical TCA-cycle enzyme aconitase 2 in mouse myoblasts and embryonic stem cells revealed that changes in the configuration of the TCA cycle accompany cell fate transitions. During exit from pluripotency, embryonic stem cells switch from canonical to non-canonical TCA-cycle metabolism. Accordingly, blocking the non-canonical TCA cycle prevents cells from exiting pluripotency. These results establish a context-dependent alternative to the traditional TCA cycle and reveal that appropriate TCA-cycle engagement is required for changes in cell state.

2021-12-01 | GSE183434 | GEO

MYC sensitises cells to apoptosis by driving energetic demand

Project description:The MYC oncogene is a potent driver of growth and proliferation but also sensitises cells to apoptosis, which limits its oncogenic potential. MYC induces several biosynthetic programmes and primary cells overexpressing MYC are highly sensitive to glutamine withdrawal suggesting that MYC-induced sensitisation to apoptosis may be due to an imbalance of metabolic/energetic supply and demand. Here we show that MYC elevates global transcription and translation, even in the absence of glutamine, revealing metabolic demand without corresponding supply. Glutamine withdrawal from MRC-5 fibroblasts depleted key TCA cycle metabolites and, in combination with MYC activation, led to AMP accumulation and nucleotide catabolism indicative of energetic stress. Further analyses revealed that glutamine supports viability through TCA cycle energetics rather than asparagine biosynthesis and that TCA cycle inhibition confers tumour suppression on MYC- driven lymphoma in vivo. In summary, glutamine supports the viability of MYC- overexpressing cells through an energetic rather than a biosynthetic mechanism.

2022-08-11 | PXD034517 | Pride

Gene expression analysis of third instar larvae ski3 mutants

Project description:Purpose: To identify genes that are differentially expressed between control and ski3 mutants Methods: Gene expressions of control and ski3 mutants of third instar larvae were generated by deep sequencing, in two replicates, using Illumina NovaSeq 6000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Bowtie2 and TopHat followed by Cufflinks. Results: We mapped 800,000-1,200,000 sequence reads per each sample to the fruit fly genome (BDGP6) and identified 93,606 transcripts in the whole body of control and ski3[f03251] with TopHat workflow. Analysis of RNA-seq data idnetified 32 differentially expressed genes relevant to mitochondrial function between control and ski3 mutants with FDR <0.05. The mutation affected over 600 genes, which are involved in many different cellular functions. The results were complex: among 32 affected genes, half of them were upregulated, and the remaining half were downregulated. Six genes were related to the TCA cycle. Of these, the downregulated genes include CG9582 (alpha-ketoglutarate transmembrane transporter), CG32832 (mitochondrial pyruvate carrier), and CG7514 (oxoglutarate:malate antiporter). On the other hand, upregulated genes include AcCoAS (Acetyl-CoA synthase), Sirup (Succinate dehydrogenase), and Men-b (malate dehydrogenase), all of which were directly involved in the TCA cycle. Conclusions: Our study represents the first detailed analysis of ski3 mutant transcriptomes, with biologic replicates, generated by RNA-seq technology. In order to examine the effects of ski3 mutations on gene expression, we performed RNA-seq analyses of wild-type and mutant larvae. Downregulation of transporter, carrier and antiporter suggested a chronic undersupply of TCA cycle substrates, while some of the TCA cycle enzymes were upregulated.

2020-01-29 | GSE144343 | GEO

Plasmodium falciparum

Project description:Gene expression analysis of a double knockout of TCA cycle enzymes IDH and KDH

| PRJNA254114 | ENA

Cell cycle-dependent gene networks for cell proliferation activated by nuclear CK2 complexes

Project description:Protein kinase CK2 is a conserved serine/threonine kinase that participates in various cellular processes. Elevated nuclear expression of CK2α has been observed in human carcinomas, but mechanisms for its variable localization in cells are poorly understood. This study demonstrates a functional connection between nuclear CK2 and gene expression in relation to cell proliferation. Growth stimulation of quiescent human fibroblasts identified a pool of CK2 highly phosphorylated at serine 7 of the α subunit that translocated into the nucleus. This phosphorylation appeared essential for its nuclear localization and catalytic activity. Protein signatures associated with nuclear CK2 complexes revealed enrichment of transcription factors and chromatin remodelers that seemed unique during progression through G1 phase of the cell cycle. Chromatin immunoprecipitation-sequencing profiling demonstrated recruitment of CK2α to the active gene locus, more abundantly in late G1 phase than in early G1. Notably, we confirmed the presence of CK2α at transcriptional start sites of core histone genes, growth stimulus-associated genes, and ribosomal RNAs. This study suggests that nuclear CK2α complexes, uniquely constituted during cell cycle progression, are essential for cell proliferation, by activating histone genes, triggering ribosome biogenesis, and then synthesize the components necessary for cell division, specified in the nucleus and also in the nucleolus.

2023-10-22 | PXD040882 | JPOST Repository

Cell cycle-dependent gene networks for cell proliferation activated by nuclear CK2 complexes

2024-10-22 | PXD046282 | JPOST Repository