scholarly journals The semi-phosphorylative Entner–Doudoroff pathway in hyperthermophilic archaea: a re-evaluation

2005 ◽  
Vol 390 (2) ◽  
pp. 529-540 ◽  
Author(s):  
Hatim Ahmed ◽  
Thijs J. G. Ettema ◽  
Britta Tjaden ◽  
Ans C. M. Geerling ◽  
John van der Oost ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Sulfolobus Solfataricus ◽  
Gene Clusters ◽  
Hyperthermophilic Archaea ◽  
Biochemical Studies ◽  
Key Enzyme ◽  
Comparative Genomics Analysis ◽  
Thermoproteus Tenax

Biochemical studies have suggested that, in hyperthermophilic archaea, the metabolic conversion of glucose via the ED (Entner–Doudoroff) pathway generally proceeds via a non-phosphorylative variant. A key enzyme of the non-phosphorylating ED pathway of Sulfolobus solfataricus, KDG (2-keto-3-deoxygluconate) aldolase, has been cloned and characterized previously. In the present study, a comparative genomics analysis is described that reveals conserved ED gene clusters in both Thermoproteus tenax and S. solfataricus. The corresponding ED proteins from both archaea have been expressed in Escherichia coli and their specificity has been identified, revealing: (i) a novel type of gluconate dehydratase (gad gene), (ii) a bifunctional 2-keto-3-deoxy-(6-phospho)-gluconate aldolase (kdgA gene), (iii) a 2-keto-3-deoxygluconate kinase (kdgK gene) and, in S. solfataricus, (iv) a GAPN (non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase; gapN gene). Extensive in vivo and in vitro enzymatic analyses indicate the operation of both the semi-phosphorylative and the non-phosphorylative ED pathway in T. tenax and S. solfataricus. The existence of this branched ED pathway is yet another example of the versatility and flexibility of the central carbohydrate metabolic pathways in the archaeal domain.

scholarly journals Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Suwen Zhao ◽  
Ayano Sakai ◽  
Xinshuai Zhang ◽  
Matthew W Vetting ◽  
Ritesh Kumar ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Large Scale ◽  
Sequence Similarity ◽  
Gene Clusters ◽  
Enzymatic Activities ◽  
Or Gene ◽  
Enzyme Functions

Metabolic pathways in eubacteria and archaea often are encoded by operons and/or gene clusters (genome neighborhoods) that provide important clues for assignment of both enzyme functions and metabolic pathways. We describe a bioinformatic approach (genome neighborhood network; GNN) that enables large scale prediction of the in vitro enzymatic activities and in vivo physiological functions (metabolic pathways) of uncharacterized enzymes in protein families. We demonstrate the utility of the GNN approach by predicting in vitro activities and in vivo functions in the proline racemase superfamily (PRS; InterPro IPR008794). The predictions were verified by measuring in vitro activities for 51 proteins in 12 families in the PRS that represent ~85% of the sequences; in vitro activities of pathway enzymes, carbon/nitrogen source phenotypes, and/or transcriptomic studies confirmed the predicted pathways. The synergistic use of sequence similarity networks3 and GNNs will facilitate the discovery of the components of novel, uncharacterized metabolic pathways in sequenced genomes.

scholarly journals USP29-mediated HIF1α stabilization is associated with Sorafenib resistance of hepatocellular carcinoma cells by upregulating glycolysis

Oncogenesis ◽  
2021 ◽  
Vol 10 (7) ◽  
Author(s):  
Ruize Gao ◽  
David Buechel ◽  
Ravi K. R. Kalathur ◽  
Marco F. Morini ◽  
Mairene Coto-Llerena ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Transcriptional Activity ◽  
Kinase Inhibitor ◽  
Aerobic Glycolysis ◽  
Hypoxia Inducible Factor ◽  
Aberrant Expression ◽  
Key Enzyme ◽  
Hcc Cells

AbstractUnderstanding the mechanisms underlying evasive resistance in cancer is an unmet medical need to improve the efficacy of current therapies. In hepatocellular carcinoma (HCC), aberrant expression of hypoxia-inducible factor 1 α (HIF1α) and increased aerobic glycolysis metabolism are drivers of resistance to therapy with the multi-kinase inhibitor Sorafenib. However, it has remained unknown how HIF1α is activated and how its activity and the subsequent induction of aerobic glycolysis promote Sorafenib resistance in HCC. Here, we report the ubiquitin-specific peptidase USP29 as a new regulator of HIF1α and of aerobic glycolysis during the development of Sorafenib resistance in HCC. In particular, we identified USP29 as a critical deubiquitylase (DUB) of HIF1α, which directly deubiquitylates and stabilizes HIF1α and, thus, promotes its transcriptional activity. Among the transcriptional targets of HIF1α is the gene encoding hexokinase 2 (HK2), a key enzyme of the glycolytic pathway. The absence of USP29, and thus of HIF1α transcriptional activity, reduces the levels of aerobic glycolysis and restores sensitivity to Sorafenib in Sorafenib-resistant HCC cells in vitro and in xenograft transplantation mouse models in vivo. Notably, the absence of USP29 and high HK2 expression levels correlate with the response of HCC patients to Sorafenib therapy. Together, the data demonstrate that, as a DUB of HIF1α, USP29 promotes Sorafenib resistance in HCC cells, in parts by upregulating glycolysis, thereby opening new avenues for therapeutically targeting Sorafenib-resistant HCC in patients.

Cellular Samurai: katanin and the severing of microtubules

2000 ◽  
Vol 113 (16) ◽  
pp. 2821-2827 ◽  
Author(s):  
L. Quarmby
Keyword(s):  
Epithelial Cells ◽  
Essential Role ◽  
Aaa Atpase ◽  
C Elegans ◽  
Microtubule Severing ◽  
Biochemical Studies ◽  
New Evidence

Recent biochemical studies of the AAA ATPase, katanin, provide a foundation for understanding how microtubules might be severed along their length. These in vitro studies are complemented by a series of recent reports of direct in vivo observation of microtubule breakage, which indicate that the in vitro phenomenon of catalysed microtubule severing is likely to be physiological. There is also new evidence that microtubule severing by katanin is important for the production of non-centrosomal microtubules in cells such as neurons and epithelial cells. Although it has been difficult to establish the role of katanin in mitosis, new genetic evidence indicates that a katanin-like protein, MEI-1, plays an essential role in meiosis in C. elegans. Finally, new proteins involved in the severing of axonemal microtubules have been discovered in the deflagellation system of Chlamydomonas.

scholarly journals T1000: A reduced toxicogenomics gene set for improved decision making

2019 ◽  
Author(s):  
Othman Soufan ◽  
Jessica Ewald ◽  
Charles Viau ◽  
Doug Crump ◽  
Markus Hecker ◽  
...  
Keyword(s):  
Dose Response ◽  
Gene Clusters ◽  
Gene Set ◽  
Chemical Hazards ◽  
Gene Sets ◽  
Toxicological Research ◽  
Multiple Species ◽  
Response Modeling

There is growing interest within regulatory agencies and toxicological research communities to develop, test, and apply new approaches, such as toxicogenomics, to more efficiently evaluate chemical hazards. Given the complexity of analyzing thousands of genes simultaneously, there is a need to identify reduced gene sets.Though several gene sets have been defined for toxicological applications, few of these were purposefully derived using toxicogenomics data. Here, we developed and applied a systematic approach to identify 1000 genes (called Toxicogenomics-1000 or T1000) highly responsive to chemical exposures. First, a co-expression network of 11,210genes was built by leveraging microarray data from the Open TG-GATEs program. This network was then re-weighted based on prior knowledge of their biological (KEGG, MSigDB) and toxicological (CTD) relevance. Finally, weighted correlation network analysis was applied to identify 258 gene clusters. T1000 was defined by selecting genes from each cluster that were most associated with outcome measures. For model evaluation, we compared the performance of T1000 to that of other gene sets (L1000, S1500, Genes selected by Limma, and random set) using two external datasets. Additionally, a smaller (T384) and a larger version (T1500) of T1000 were used for dose-response modeling to test the effect of gene set size. Our findings demonstrated that the T1000 gene set is predictive of apical outcomes across a range of conditions (e.g.,in vitroand in vivo, dose-response, multiple species, tissues, and chemicals), and generally performs as well, or better than other gene sets available.

scholarly journals Phosphatidylcholine Synthesis Influences the Diacylglycerol Homeostasis Required for Sec14p-dependent Golgi Function and Cell Growth

2001 ◽  
Vol 12 (3) ◽  
pp. 511-520 ◽  
Author(s):  
Annette L. Henneberry ◽  
Thomas A. Lagace ◽  
Neale D. Ridgway ◽  
Christopher R. McMaster
Keyword(s):  
Cell Death ◽  
Cell Growth ◽  
Phosphatidic Acid ◽  
Metabolic Pathways ◽  
Eukaryotic Cells ◽  
Kennedy Pathway ◽  
Phosphatidylcholine Synthesis ◽  
Long Chain

Phosphatidylcholine and phosphatidylethanolamine are the most abundant phospholipids in eukaryotic cells and thus have major roles in the formation and maintenance of vesicular membranes. In yeast, diacylglycerol accepts a phosphocholine moiety through aCPT1-derived cholinephosphotransferase activity to directly synthesize phosphatidylcholine. EPT1-derived activity can transfer either phosphocholine or phosphoethanolamine to diacylglcyerol in vitro, but is currently believed to primarily synthesize phosphatidylethanolamine in vivo. In this study we report that CPT1- and EPT1-derived cholinephosphotransferase activities can significantly overlap in vivo such that EPT1 can contribute to 60% of net phosphatidylcholine synthesis via the Kennedy pathway. Alterations in the level of diacylglycerol consumption through alterations in phosphatidylcholine synthesis directly correlated with the level of SEC14-dependent invertase secretion and affected cell viability. Administration of synthetic di8:0 diacylglycerol resulted in a partial rescue of cells fromSEC14-mediated cell death. The addition of di8:0 diacylglycerol increased di8:0 diacylglycerol levels 20–40-fold over endogenous long-chain diacylglycerol levels. Di8:0 diacylglcyerol did not alter endogenous phospholipid metabolic pathways, nor was it converted to di8:0 phosphatidic acid.

Bioconversion of Carbon Monoxide to Formate Using Artificially Designed Carbon Monoxide:Formate Oxidoreductase in Hyperthermophilic Archaea

2021 ◽  
Author(s):  
Jae Kyu Lim ◽  
Ji-In Yang ◽  
Yun Jae Kim ◽  
Yeong-Jun Park ◽  
Yong Hwan Kim
Keyword(s):  
Carbon Monoxide ◽  
Electron Transfer ◽  
Fusion Protein ◽  
Direct Electron Transfer ◽  
Co2 Reduction ◽  
Hyperthermophilic Archaea ◽  
Production Activity ◽  
Formate Production

Abstract Ferredoxin-dependent metabolic engineering of electron transfer circuits has been developed to enhance redox efficiency in the field of synthetic biology, e.g., for hydrogen production and for reduction of flavoproteins or NAD(P)+. Here, we present the bioconversion of carbon monoxide (CO) gas to formate via a synthetic CO:formate oxidoreductase (CFOR), designed as an enzyme complex for direct electron transfer between noninteracting CO dehydrogenase and formate dehydrogenase using an electron-transferring Fe-S fusion protein. The CFOR-introduced Thermococcus onnurineus mutant strains showed CO-dependent formate production in vivo and in vitro. The formate production rate from purified CFOR complex and specific formate productivity from the bioreactor were 348 ± 34 μmol/mg/min and 90.2 ± 20.4 mmol/g-cells/h, respectively. The CO-dependent CO2 reduction/formate production activity of synthetic CFOR was confirmed, indicating that direct electron transfer between two unrelated dehydrogenases was feasible via mediation of the FeS-FeS fusion protein.

Abstract 14532: Computational Drug Repurposing Identifies a Piperlongumine Analog That Controls a Gstp1-iscu Pathogenic Axis in Pulmonary Hypertension

Circulation ◽  
2020 ◽  
Vol 142 (Suppl_3) ◽  
Author(s):  
Jimin Yang
Keyword(s):  
Drug Repurposing ◽  
Gene Clusters ◽  
Loss Of Function ◽  
Sequencing Data ◽  
Glutathione S Transferase ◽  
Computational Screening ◽  
Therapeutic Development ◽  
Pulmonary Arterial

Background and Hypothesis: Pulmonary arterial hypertension (PAH) is an incurable vascular disease for which chemotherapies are being considered for therapeutic development. There is no method reported to date for effective computational screening of these drugs for this disease. Big data analyses that leverage the molecular parallels between cancer and PH may define novel pathogenic mechanisms and facilitate repurposing of chemotherapies for PAH. More specifically, while functional deficiency of the iron-sulfur (Fe-S) biogenesis gene ISCU and oxidative metabolism in human pulmonary arterial endothelial cells (PAECs) is known to drive PAH, the pathogenic regulation of ISCU is not fully defined, and no tailored drugs have been identified to bolster ISCU activity. Methods and Results: We applied a computational algorithm EDDY (Evaluating Differential DependencY), which analyzes RNA sequencing data from 810 cancer cell lines exposed to 368 small molecules, in order to identify chemotherapeutics that depended upon rewired PH-related gene clusters. The top ranked drug was a piperlongumine (PL) analog (BRD2889) that was predicted to extensively rewire dependencies across PH gene clusters, mediated by ISCU. In vitro, coupling gain- and loss-of-function analyses of GSTP1 with BRD2889 exposure in PAECs, we found that BRD2889 inhibits glutathione S-transferase P1 (GSTP1), an enzyme which in turn catalyzes ISCU glutathionylation and increases its stability in hypoxia. Consequently, BRD2889 and GSTP1 knockdown phenocopy one another by increasing Fe-S-dependent Complex I activity and mitochondrial oxygen consumption while ameliorating pathogenic apoptosis. Consistent with these computational and in vitro results, in a mouse model of PAH (IL-6 transgenic mice in hypoxia), BRD2889 improved hemodynamic and molecular disease manifestations in vivo. Conclusions: Using a novel computational platform, we identified a coordinated connection between BRD342289 and GSTP1-ISCU axis, crucial to PAEC metabolism. This study offers insight to fundamental PH pathobiology and sets the stage for accelerated repurposing of chemotherapies such as BRD342289 in PH.

scholarly journals Effects of indole-3-carbinol on metabolic parameters and on lipogenesis and lipolysis in adipocytes 182

2009 ◽  
Vol 54 (No. 4) ◽  
pp. 182-189 ◽  
Author(s):  
M. Okulicz ◽  
I. Hertig ◽  
J. Chichłowska
Keyword(s):  
Metabolic Pathways ◽  
Direct Action ◽  
Liver Steatosis ◽  
Density Lipoprotein ◽  
Metabolic Parameters ◽  
Male Rats ◽  
Liver Cholesterol ◽  
Carbohydrate And Lipid Metabolism

: Indole-3-carbinol (I3C) was found to have possible anticarcinogenic, antioxidant and anti-atherogenic effects on the organism. So far, its influence on metabolic pathways has been unknown. This work was the first attempt to determine the carbohydrate and lipid metabolism changes <I>in vivo</I> after administration of 150 mg/kg b.wt./day I3C to male rats. Additionally, the aim of this trial was to evaluate the direct effect of I3C on basal and hormone-induced lipogenesis and lipolysis in isolated rat adipocytes at concentrations 1, 10, 100 &mu;M <I>in vitro</I>. We can corroborate that adipocytes are susceptible to the direct action of I3C. The incubation of adipocytes with I3C at the three above-mentioned concentrations resulted in its influence on restriction of glucose entry into adipocytes in the basal as well as insulin-stimulated conditions. However, it was observed that I3C at these concentrations strongly intensified basic and epinephrine-stimulated lipolysis. I3C also has a significant influence on metabolism <I>in vivo</I>. Its administration to rats caused a significant increase in the content of triglycerides and a decrease in glycogen in the liver. The considerable augmentation of glucose, triglycerides, cholesterol in high-density lipoprotein and insulin with a concomitant decrease in FFA concentrations was noted in the blood serum. I3C did not alter phospholipids, total, free, esterified cholesterol in the serum and the liver cholesterol. The results obtained <I>in vivo</I> and <I>in vivo</I> indicate that the effect of I3C is adverse for the majority of metabolic parameters which were investigated. The most important finding in this study is the effect of I3C on liver steatosis and that the observed lower lipogenesis at higher lipolysis in fat cells may be involved in the mechanism.

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