R-Lipoic Acid Inhibits Mammalian Pyruvate Dehydrogenase Kinase
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Synthetic Analogues of 2-Oxo Acids Discriminate Metabolic Contribution of the 2-Oxoglutarate and 2-Oxoadipate Dehydrogenases in Mammalian Cells and Tissues Artem V
www.nature.com/scientificreports OPEN Synthetic analogues of 2-oxo acids discriminate metabolic contribution of the 2-oxoglutarate and 2-oxoadipate dehydrogenases in mammalian cells and tissues Artem V. Artiukhov1,2, Aneta Grabarska3, Ewelina Gumbarewicz3, Vasily A. Aleshin1,2, Thilo Kähne4, Toshihiro Obata5,7, Alexey V. Kazantsev6, Nikolay V. Lukashev6, Andrzej Stepulak3, Alisdair R. Fernie5 & Victoria I. Bunik1,2* The biological signifcance of the DHTKD1-encoded 2-oxoadipate dehydrogenase (OADH) remains obscure due to its catalytic redundancy with the ubiquitous OGDH-encoded 2-oxoglutarate dehydrogenase (OGDH). In this work, metabolic contributions of OADH and OGDH are discriminated by exposure of cells/tissues with diferent DHTKD1 expression to the synthesized phosphonate analogues of homologous 2-oxodicarboxylates. The saccharopine pathway intermediates and phosphorylated sugars are abundant when cellular expressions of DHTKD1 and OGDH are comparable, while nicotinate and non-phosphorylated sugars are when DHTKD1 expression is order(s) of magnitude lower than that of OGDH. Using succinyl, glutaryl and adipoyl phosphonates on the enzyme preparations from tissues with varied DHTKD1 expression reveals the contributions of OADH and OGDH to oxidation of 2-oxoadipate and 2-oxoglutarate in vitro. In the phosphonates-treated cells with the high and low DHTKD1 expression, adipate or glutarate, correspondingly, are the most afected metabolites. The marker of fatty acid β-oxidation, adipate, is mostly decreased by the shorter, OGDH-preferring, phosphonate, in agreement with the known OGDH dependence of β-oxidation. The longest, OADH- preferring, phosphonate mostly afects the glutarate level. Coupled decreases in sugars and nicotinate upon the OADH inhibition link the perturbation in glucose homeostasis, known in OADH mutants, to the nicotinate-dependent NAD metabolism. -
Critical Assessment of Human Metabolic Pathway Databases: a Stepping Stone for Future Integration Stobbe Et Al
Critical assessment of human metabolic pathway databases: a stepping stone for future integration Stobbe et al. Stobbe et al. BMC Systems Biology 2011, 5:165 http://www.biomedcentral.com/1752-0509/5/165 (14 October 2011) Stobbe et al. BMC Systems Biology 2011, 5:165 http://www.biomedcentral.com/1752-0509/5/165 RESEARCHARTICLE Open Access Critical assessment of human metabolic pathway databases: a stepping stone for future integration Miranda D Stobbe1,3, Sander M Houten5,6, Gerbert A Jansen1,3, Antoine HC van Kampen1,2,3,4 and Perry D Moerland1,3* Abstract Background: Multiple pathway databases are available that describe the human metabolic network and have proven their usefulness in many applications, ranging from the analysis and interpretation of high-throughput data to their use as a reference repository. However, so far the various human metabolic networks described by these databases have not been systematically compared and contrasted, nor has the extent to which they differ been quantified. For a researcher using these databases for particular analyses of human metabolism, it is crucial to know the extent of the differences in content and their underlying causes. Moreover, the outcomes of such a comparison are important for ongoing integration efforts. Results: We compared the genes, EC numbers and reactions of five frequently used human metabolic pathway databases. The overlap is surprisingly low, especially on reaction level, where the databases agree on 3% of the 6968 reactions they have combined. Even for the well-established tricarboxylic acid cycle the databases agree on only 5 out of the 30 reactions in total. -
The Enzyme Database: New Enzymes 06/27/2006 05:11 PM
The Enzyme Database: New Enzymes 06/27/2006 05:11 PM Home Search Enzymes by Class New/Amended Enzymes Statistics Forms Advanced Search Information Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) Proposed Changes to the Enzyme List The entries below are proposed additions and amendments to the Enzyme Nomenclature list. They were prepared for the NC- IUBMB by Keith Tipton, Sinéad Boyce, Gerry Moss and Hal Dixon, with occasional help from other Committee members, and were put on the web by Gerry Moss. Comments and suggestions on these draft entries should be sent to Professor K.F. Tipton and Dr S. Boyce (Department of Biochemistry, Trinity College Dublin, Dublin 2, Ireland) by 20 May 2006, after which, the entries will be made official and will be incorporated into the main enzyme list. To prevent confusion please do not quote new EC numbers until they are incorporated into the main list. Many thanks to those of you who have submitted details of new enzymes or updates to existing enzymes. An asterisk before 'EC' indicates that this is an amendment to an existing enzyme rather than a new enzyme entry. Contents *EC 1.1.1.262 4-hydroxythreonine-4-phosphate dehydrogenase EC 1.1.1.289 sorbose reductase EC 1.1.1.290 4-phosphoerythronate dehydogenase EC 1.1.99.19 transferred *EC 1.2.1.10 acetaldehyde dehydrogenase (acetylating) EC 1.2.1.71 succinylglutamate-semialdehyde dehydrogenase EC 1.2.1.72 erythrose-4-phosphate dehydrogenase EC 1.2.99.1 transferred *EC 1.3.99.19 quinoline-4-carboxylate 2-oxidoreductase -
Supplemental Figures 04 12 2017
Jung et al. 1 SUPPLEMENTAL FIGURES 2 3 Supplemental Figure 1. Clinical relevance of natural product methyltransferases (NPMTs) in brain disorders. (A) 4 Table summarizing characteristics of 11 NPMTs using data derived from the TCGA GBM and Rembrandt datasets for 5 relative expression levels and survival. In addition, published studies of the 11 NPMTs are summarized. (B) The 1 Jung et al. 6 expression levels of 10 NPMTs in glioblastoma versus non‐tumor brain are displayed in a heatmap, ranked by 7 significance and expression levels. *, p<0.05; **, p<0.01; ***, p<0.001. 8 2 Jung et al. 9 10 Supplemental Figure 2. Anatomical distribution of methyltransferase and metabolic signatures within 11 glioblastomas. The Ivy GAP dataset was downloaded and interrogated by histological structure for NNMT, NAMPT, 12 DNMT mRNA expression and selected gene expression signatures. The results are displayed on a heatmap. The 13 sample size of each histological region as indicated on the figure. 14 3 Jung et al. 15 16 Supplemental Figure 3. Altered expression of nicotinamide and nicotinate metabolism‐related enzymes in 17 glioblastoma. (A) Heatmap (fold change of expression) of whole 25 enzymes in the KEGG nicotinate and 18 nicotinamide metabolism gene set were analyzed in indicated glioblastoma expression datasets with Oncomine. 4 Jung et al. 19 Color bar intensity indicates percentile of fold change in glioblastoma relative to normal brain. (B) Nicotinamide and 20 nicotinate and methionine salvage pathways are displayed with the relative expression levels in glioblastoma 21 specimens in the TCGA GBM dataset indicated. 22 5 Jung et al. 23 24 Supplementary Figure 4. -
Lipoate-Binding Proteins and Specific Lipoate-Protein Ligases in Microbial
RESEARCH ARTICLE Lipoate-binding proteins and specific lipoate-protein ligases in microbial sulfur oxidation reveal an atpyical role for an old cofactor Xinyun Cao1†‡, Tobias Koch2†, Lydia Steffens2, Julia Finkensieper2, Renate Zigann2, John E Cronan1,3, Christiane Dahl2* 1Department of Biochemistry, University of Illinois, Urbana, United States; 2Institut fu¨ r Mikrobiologie and Biotechnologie, Rheinische Friedrich-Wilhelms-Universita¨ t Bonn, Bonn, Germany; 3Department of Microbiology, University of Illinois, Urbana, United States Abstract Many Bacteria and Archaea employ the heterodisulfide reductase (Hdr)-like sulfur oxidation pathway. The relevant genes are inevitably associated with genes encoding lipoate- binding proteins (LbpA). Here, deletion of the gene identified LbpA as an essential component of the Hdr-like sulfur-oxidizing system in the Alphaproteobacterium Hyphomicrobium denitrificans. *For correspondence: Thus, a biological function was established for the universally conserved cofactor lipoate that is [email protected] markedly different from its canonical roles in central metabolism. LbpAs likely function as sulfur- binding entities presenting substrate to different catalytic sites of the Hdr-like complex, similar to †These authors contributed the substrate-channeling function of lipoate in carbon-metabolizing multienzyme complexes, for equally to this work example pyruvate dehydrogenase. LbpAs serve a specific function in sulfur oxidation, cannot ‡ Present address: Department functionally replace the related GcvH protein in Bacillus subtilis and are not modified by the of Biochemistry, University of canonical E. coli and B. subtilis lipoyl attachment machineries. Instead, LplA-like lipoate-protein Wisconsin-Madison, Madison, ligases encoded in or in immediate vicinity of hdr-lpbA gene clusters act specifically on these United States proteins. Competing interests: The DOI: https://doi.org/10.7554/eLife.37439.001 authors declare that no competing interests exist. -
Chronic Inhibition of Mitochondrial Dihydrolipoamide Dehydrogenase (DLDH) As an Approach to Managing Diabetic Oxidative Stress
antioxidants Perspective Chronic Inhibition of Mitochondrial Dihydrolipoamide Dehydrogenase (DLDH) as an Approach to Managing Diabetic Oxidative Stress Xiaojuan Yang, Jing Song and Liang-Jun Yan * Department of Pharmaceutical Sciences, UNT System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, TX 76107, USA; [email protected] (X.Y.); [email protected] (J.S.) * Correspondence: [email protected]; Tel.: +1-817-735-2386; Fax: +1-817-735-2603 Received: 11 January 2019; Accepted: 28 January 2019; Published: 2 February 2019 Abstract: Mitochondrial dihydrolipoamide dehydrogenase (DLDH) is a redox enzyme involved in decarboxylation of pyruvate to form acetyl-CoA during the cascade of glucose metabolism and mitochondrial adenine triphosphate (ATP) production. Depending on physiological or pathophysiological conditions, DLDH can either enhance or attenuate the production of reactive oxygen species (ROS) and reactive nitrogen species. Recent research in our laboratory has demonstrated that inhibition of DLDH induced antioxidative responses and could serve as a protective approach against oxidative stress in stroke injury. In this perspective article, we postulated that chronic inhibition of DLDH could also attenuate oxidative stress in type 2 diabetes. We discussed DLDH-involving mitochondrial metabolic pathways and metabolic intermediates that could accumulate upon DLDH inhibition and their corresponding roles in abrogating oxidative stress in diabetes. We also discussed a couple of DLDH inhibitors that could be tested in animal models of type 2 diabetes. It is our belief that DLDH inhibition could be a novel approach to fighting type 2 diabetes. Keywords: diabetes mellitus; dihydrolipoamide dehydrogenase; mitochondria; oxidative stress; reactive oxygen species 1. Introduction Adult-onset diabetes mellitus, also known as type 2 diabetes, is caused by insulin resistance followed by β-cell dysfunction [1–3].