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Nucleoside-Diphosphate Kinase 1 and 2 are master regulators of a liver protective response to high fat diet [ChIP-seq]

ABSTRACT: Nucleoside-Diphosphate Kinase 1 and 2 are master regulators of a liver protective response to high fat diet [ChIP-seq]

PROVIDER: PRJNA816470 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18331904_1.fastq.gz	Fastqsanger.gz
	SRR18331904_2.fastq.gz	Fastqsanger.gz
	SRR18331905_1.fastq.gz	Fastqsanger.gz
	SRR18331905_2.fastq.gz	Fastqsanger.gz
	SRR18331906_1.fastq.gz	Fastqsanger.gz

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Similar Datasets

Nucleoside-Diphosphate Kinase 1 and 2 are master regulators of a liver protective response to high fat diet.

Project description:Nucleoside-Diphosphate Kinase 1 and 2 are master regulators of a liver protective response to high fat diet.

| PRJNA816457 | ENA

Nucleoside-Diphosphate Kinase 1 and 2 are master regulators of a liver protective response to high fat diet [RNA-seq]

Project description:Nucleoside-Diphosphate Kinase 1 and 2 are master regulators of a liver protective response to high fat diet [RNA-seq]

| PRJNA816471 | ENA

Nucleoside-Diphosphate Kinase 1 and 2 are master regulators of a liver protective response to high fat diet [RNA-seq]

Project description:Fatty acid homeostasis is critical for normal cellular physiology and leads to severe diseases when deregulated. Here we report Nucleoside-Diphosphate Kinase 1 and 2 (NME1/2) as major cellular co-enzyme A (CoA) and acetyl-CoA binding proteins and negative regulators of de novo lipogenesis (DNL). Structural studies demonstrate that Nme1 recognizes CoA through its nucleotide moiety, which competes for binding with ADP/ATP. By using a Nme2 ko mouse model, we observe that NME2 is required for the gene transcriptional response to a high fat diet (HFD) in liver cells, leading to a repression of lipogenesis and the activation of a protective gene response. Nme2 ko mice submitted to a HFD challenge are unable to repress key lipogenic genes, resulting in an excessive triglyceride synthesis and liver steatosis. Mechanistically, the NME2-dependent down-regulation of DNL in response to HFD changes the balance for the use of acetyl-CoA between the competing paths of acetylation and DNL, thereby increasing TSS-targeted histone acetylation and gene activation. A structure-guided generation of a NME1 mutant, with intact NDK activity, but unable to bind CoA, directly demonstrates the functional impact of acetyl-CoA/CoA binding by NME1/2 in repressing DNL. Taken together, these findings highlight a yet unknow protective liver response to HFD, regulated by multi-ligand binding proteins which act as direct sensors for the cellular levels of NDP/NTP and CoA/acetyl-CoA.

2023-08-01 | GSE198686 | GEO

Nucleoside-Diphosphate Kinase 1 and 2 are master regulators of a liver protective response to high fat diet [ChIP-seq]

2023-08-01 | GSE198687 | GEO

Nucleoside diphosphate kinase A (NME1) catalyzes its own oligophosphorylation

Project description:Protein phosphorylation is a central regulatory mechanism in eukaryotic cell signaling, and was recently expanded to include protein pyrophosphorylation and protein polyphosphorylation. Here, we report the discovery of yet another mode of phosphorylation – protein oligophosphorylation. Using site-specifically phosphorylated and pyrophosphorylated nucleoside diphosphate kinase A (NME1), the effects of these modifications on enzyme activity were investigated. Phosphorylation, and even more so pyrophosphorylation, on threonine 94 notably reduced the nucleoside diphosphate kinase activity. Nevertheless, both phosphoprotein and pyrophosphoprotein were able to catalyze their own oligophosphorylation – up to the formation of a hexaphosphate chain – using ATP as a co-factor. This reaction was critically dependent on the catalytic histidine residue (H118) and cryo-EM analysis of the differently modified proteins suggests an intramolecular phosphoryl transfer, likely via a phosphohistidine intermediate. Oligophosphorylation of NME1 in biochemical samples, as well as cell lysates, was further confirmed using mass spectrometry, and oligophophorylation promoted a new set of protein interactions. Our results highlight the complex nature of phosphoregulation, and the methods described here provide the opportunity to investigate the occurrence and the impact of this novel modification in the future.

2025-08-21 | PXD054175 | Pride

Nucleoside-Diphosphate Kinase 1 and 2 (Nme1/2) are major cellular co-enzyme A/acetyl-CoA binding factors

Project description:Co-enzyme A is the essential cellular carrier of the acetyl group, largely used in fatty acid synthesis and lysine post-translational modifications of proteins. Following the analysis of the cellular CoA-binding proteome, we identified Nme1/2 as major abundant cytoplasmic CoA-binding proteins. We report a novel mechanism that controls fatty acids synthesis involving ATP-dependent acetyl-CoA binding by Nucleoside Diphosphate Kinases 1 and 2 (Nme1/2).

2023-08-01 | PXD029159 | Pride

Nucleoside-Diphosphate Kinase 1 and 2 are master regulators of a liver protective response to high fat diet.

Project description:This SuperSeries is composed of the SubSeries listed below.

2023-08-01 | GSE198688 | GEO

Modulation of abiotic stress tolerance and photosynthesis of cyanobacterium Nostoc PCC 7120 through altered phosphoproteome mediated by Nucleoside diphosphate kinase

Project description:Nucleoside diphosphate kinase (Ndk/NDK/NDPK) is known to possess pleiotropic functions, one of which is that as a protein kinase, and known to be involved in stress tolerance in plants. The role of Ndk in the ancient cyanobacteria, also known as the progenitor of chloroplast, has not been investigated. To assess the role in Nostoc PCC 7120, a recombinant strain overexpressing Ndk, Anndk+ was generated. Phosphoproteomic analysis of Anndk+ and its comparison with that of the vector control AnpAM revealed differential phosphorylation at S/T/Y sites of proteins belonging to varied functional groups, with the majority being from those involved in photosynthesis. A total of 177 phosphopeptides and 117 phosphoproteins were identified, some of which have been identified as a phosphopeptide for the first time in any cyanobacteria. Compared to AnpAM, the Anndk+ cells exhibited (i) lower photosynthetic efficiency and electron transport rate at low PAR (photosynthetically active radiation), (ii) no change in photochemical quenching across PAR, (iii) but distinct non-photochemical quenching [zero Y(NPQ) and high Y(NO) in Anndk+ and high Y(NPQ) and low (NO) in AnpAM], and (iv) increased tolerance to -radiation, oxidative, salt and DCMU stresses. The possible role of the change in phosphoproteome of Nostoc upon overexpression of Ndk in modulating photosynthetic parameters and abiotic stress tolerance has been discussed. This is the first report on a wide physiological role for nucleoside diphosphate kinase in any cyanobacteria.

2025-05-06 | PXD050799 | Pride

Knockdown of the nucleoside diphosphate linked moiety X-type motif Nudt19 increases fatty acid oxidation and ATP production in murine liver cells

Project description:Changes in intracellular CoA levels are known to contribute to the development of non-alcoholic fatty liver disease (NAFLD) in type 2 diabetes (T2D). The underlying genetic basis for the development and progression of these complex disorders, however, is still poorly understood. Due to their diverse susceptibility towards metabolic diseases, mouse inbred strains have been proven to serve as powerful tools in the identification of novel genetic factors that are fundamental in the pathophysiology of diabetes and NAFLD. Transcriptome analysis revealed the nucleoside diphosphate linked moiety X type motif Nudt19 as novel candidate gene responsible for NAFLD and T2D development. Knockdown (KD) of Nudt19 increased both mitochondrial and glycolytic ATP production rates in Hepa 1-6 cells. The enforced utilization of glutamine or fatty acids as energy substrate reduced uncoupled respiration in NT cells. This reduction was prevented upon knockdown of Nudt19. Furthermore, incubation with palmitate or oleate increased mitochondrial ATP production and uncoupled respiration in Nudt19 KD cells, but not in NT cells. The enhanced fatty acid oxidation in Nudt19 KD cells was accompanied by an increased abundance of Pdk4. This study describes for the first time Nudt19 as regulator of hepatic lipid metabolism and potential mediator of NAFLD and T2D development.

2022-04-11 | GSE186106 | GEO

Regulators of mitonuclear balance link mitochondrial metabolism to mtDNA expression

Project description:Mitochondrial oxidative phosphorylation (OXPHOS) complexes are assembled from proteins encoded by both nuclear and mitochondrial DNA. These dual-origin enzymes pose a complex gene regulatory challenge for cells requiring coordinated gene expression across organelles. To identify genes involved in dual-origin protein complex synthesis, we performed fluorescence-activated cell-sorting-based genome-wide screens analysing mutant cells with unbalanced levels of mitochondrial- and nuclear-encoded subunits of Complex IV. We identified genes involved in OXPHOS biogenesis, including two uncharacterized genes: PREPL and NME6. We found that PREPL specifically impacts Complex IV biogenesis by acting at the intersection of mitochondrial lipid metabolism and protein synthesis, whereas NME6, an uncharacterized nucleoside diphosphate kinase, controls OXPHOS biogenesis through multiple mechanisms reliant on its NDPK domain. Firstly, NME6 forms a complex with RCC1L, which together perform nucleoside diphosphate kinase activity to maintain local mitochondrial pyrimidine triphosphate levels essential for mitochondrial RNA abundance. Secondly, NME6 modulates the activity of mitoribosome regulatory complexes, altering mitoribosome assembly and mitochondrial RNA pseudouridylation. Taken together, we propose that NME6 acts as a link between compartmentalized mitochondrial metabolites and mitochondrial gene expression.

2023-08-17 | GSE224503 | GEO

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