Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1294558 | ENA |
REPOSITORIES: ENA
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Project description:Naphthoquinones preferentially pair with the non-proton-pumping NADH dehydrogenase, thereby optimizing electron transport in low-potential respiratory chains under aerobic conditions.
2025-09-15 | GSE303520 | GEO
Project description:RNA-Seq results accompanying submission of a manuscript: "The orphan response regulator Rv3143 modulates the activity of the NADH dehydrogenase complex (Nuo) in Mycobacterium tuberculosis via protein-protein interactions" describing the function of the Rv3143 "orphan" response regulator of the two-component signal transduction systems family, which enable mycobacterial cells to quickly adapt and adequately respond to adverse environmental conditions encountered at various stages of host infection. We identified the Rv3143 protein as an interaction partner for NADH dehydrogenase complex involved in oxidative phosphorylation. We propose that the regulatory protein Rv3143 is a component of the complex and modulates its activity.
2022-06-01 | GSE193950 | GEO
Project description:Previous findings have demonstrated that the NADH/NAD+ ratio has a strong impact on the glycolytic flux in C. glutamicum under anaerobic conditions in the absence of external electron acceptors. During an attempt to rewire anaerobic metabolism to achieve high yield formation of ethanol, we inactivated the malate dehydrogenase and lactate dehydrogenase in a C. glutamicum strain expressing pyruvate decarboxylase and alcohol dehydrogenase, to eliminate formation of the by-products succinate and lactate, respectively. This modification increased the yield of ethanol but had a negative effect on glycolysis, which we found to correlate with an elevated NADH/NAD+ ratio. The pyruvate dehydrogenase (PDH) of C. glutamicum is active under anaerobic conditions, and can potentially exacerbate the negative effect on glycolysis, due to NADH formation. To reduce PDH activity under anaerobic conditions, we decided to replace the gene encoding the E3 subunit of PDH with its Escherichia coli counterpart, as E. coli PDH has been reported to be functional under aerobic conditions only. The resultant strain JS133 produced far less acetate with a further increased ethanol production, however, the glycolytic flux was still low. After observing differences in glycolytic flux for JS133 on glucose and fructose, we speculated that the pentose phosphate pathway (PPP) might be involved in the reduced flux on glucose. To prove this, we deleted the zwf gene, encoding glucose-6-phosphate dehydrogenase, which is the entry point into PPP, and immediately observed a stimulating effect on glycolysis. Subsequent characterization revealed a direct correlation between the intracellular NADH/NAD+ and NADPH/NADP+ ratios under anoxic conditions. Based on these findings we managed to re-channel the metabolism of C. glutamicum successfully towards either to ethanol or D-lactate with 92% and 98% of the theoretical yield respectively, which is the highest yields for D-lactate production thus far reported in the literature.
2020-10-02 | GSE143977 | GEO
Project description:Naphthoquinone preferentially pairs with non-proton-pumping NADH dehydrogenase for respiratory electron transport
| PRJNA1295560 | ENA
Project description:We previously reported that a recombinant Candida utilis strain expressing a Candida shehatae xylose reductase K275R/N277D, a C. shehatae xylitol dehydrogenase, and xylulokinase from Pichia stipitis produced ethanol from xylose. However, its productivity was low. In this study, metabolomic (CE-TOF MS) and transcriptomic (microarray) analyses were performed to characterize xylose metabolism by the engineered C. utilis and to identify key genetic changes contributing to efficient xylose utilization. Metabolomic analysis revealed that the xylose-fermenting strain accumulated more pentose phosphate pathway intermediates, more NADH, and more glycolytic intermediates upstream of glyceraldehyde 3-phosphate than wild-type. Transcriptomic analysis of the strain grown on xylose indicated a significant increase in expression of genes encoding tricarboxylic acid cycle enzymes, respiratory enzymes, and enzymes involved in ethanol oxidation. To decrease the NADH/NAD+ ratio and increase ethanol yield from the fermentation of xylose, ADH1 encoding NADH-dependent alcohol dehydrogenase was overexpressed. The resultant strain exhibited a 17% increase in ethanol production and a 22% decrease in xylitol accumulation relative to the control.
2014-01-01 | GSE43514 | GEO
Project description:The oxidation of NADH is essential for maintaining cellular redox balance and supporting cell metabolism. Mitochondrial complex I (NADH:ubiquinone oxidoreductase) plays a central role in this process by coupling NADH oxidation to electron transfer and protons translocation across the inner mitochondrial membrane. We previously reported that the antiseizure drug stiripentol decreases lactate production and mitochondrial respiration, suggesting an impact on NADH turnover beyond its known inhibition of lactate dehydrogenase. In this study, we identify complex I as a target of stiripentol across multiple species and cell types. Biochemical and spectroscopic analyses demonstrate that stiripentol inhibits NADH oxidation and electron transfer through a mechanism distinct from that of classical ubiquinone pocket inhibitors such as rotenone or piericidin A. Remarkably, stiripentol acts upstream of the ubiquinone reduction site, representing the first example of a complex I inhibitor with a binding site within the N-module. These findings uncover a previously unrecognized mode of complex I inhibition and link stiripentol’s metabolic effects to direct modulation of mitochondrial NADH oxidation. This work broadens the understanding of stiripentol’s mechanism of action and highlights its potential to modulate redox metabolism in cancer cells.
2026-01-29 | GSE317932 | GEO
Project description:We aimed to identify the approximate binding position of the NADH dehydrogenase Nde1 on the respiratory supercomplex.
2026-03-04 | PXD061923 | Pride
Project description:We used single nuclei RNA-seq to compare gene expression from adipocyte circadian mutant mice +/- expression of the yeast NADH dehydrogenase (NDI1). We used RNA-sequencing of fractionated adipocytes from the visceral white adipose tissue of control mice, mice lacking the circadian clock activator Bmal1, and mice lacking the mitochondrial complex I subunit Ndufs2.
2026-01-05 | GSE245850 | GEO
Project description:Metabolic cofactors such as NADH and ATP play important roles in a large number of cellular reactions and it is of great interest to dissect the role of these cofactors in different aspects of metabolism. Towards this goal, we overexpressed NADH oxidase and the soluble F1-ATPase in Escherichia coli to lower the level of NADH and ATP, respectively. We used a systems biology approach to study the response to these perturbations by measuring global transcription profiles, metabolic fluxes and the metabolite levels. We integrated information from the different measurements using network-based methods to identify high-scoring networks in a global interaction map that included protein interactions, transcriptional regulation and metabolism. The results revealed that the action of many global transcription factors such as ArcA, Fnr, CRP and IHF commonly involved both NADH and ATP while others were influential only in one of the pertubations. In general, overexpressing NADH oxidase invokes response in widespread aspects of metabolism involving the redox cofactors (NADH and NADPH) while ATPase has a more focused response to restore ATP level by enhancing proton translocation mechanisms and repressing biosynthesis. Interestingly, NADPH played a key role in restoring redox homeostasis through the concerted activity of isocitrate dehydrogenase and UdhA transhydrogenase. We present a reconciled network of regulation that illustrates the overlapping and distinct aspects of metabolism controlled by NADH and ATP. Our study contributes to the general understanding of redox and energy metabolism and should help in developing metabolic engineering strategies in E. coli.
2010-02-18 | GSE20374 | GEO
Project description:Respiratory complex I (NADH:ubiquinone oxidoreductase) is essential for cellular energy production and NAD+ homeostasis. Complex I mutations cause neuromuscular, mitochondrial diseases, such as Leigh Syndrome, but their molecular-level consequences remain poorly understood. Here, we use a popular complex I-linked mitochondrial disease model, the ndufs4-/- mouse, to define the structural, biochemical and functional consequences of the absence of subunit NDUFS4. Cryo-EM analyses of mouse-heart ndufs4-/- complex I revealed a loose association of the NADH-dehydrogenase module, and discrete classes containing either assembly factor NDUFAF2 or subunit NDUFS6. Subunit NDUFA12 (that replaces its paralogue NDUFAF2 in mature complex I) is absent from all classes, compounding the deletion of NDUFS4 and preventing maturation of an NDUFS4-free but otherwise complete enzyme. We propose NDUFAF2 as the major recruiter of the NADH-dehydrogenase module during assembly of the complex. Our results provide new molecular-level understanding of the ndufs4-/- mouse model and complex I-linked mitochondrial disease.
2024-01-02 | PXD044975 | Pride