Glycolytic Enzymes and Glucose-6-Phosphate Dehydrogenase
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Eradication of ENO1-Deleted Glioblastoma Through Collateral Lethality
bioRxiv preprint doi: https://doi.org/10.1101/331538; this version posted May 25, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Eradication of ENO1-deleted Glioblastoma through Collateral Lethality Yu-Hsi Lin1, Nikunj Satani1,2, Naima Hammoudi1, Jeffrey J. Ackroyd1, Sunada Khadka1, Victoria C. Yan1, Dimitra K. Georgiou1, Yuting Sun3, Rafal Zielinski4, Theresa Tran1, Susana Castro Pando1, Xiaobo Wang1, David Maxwell5, Zhenghong Peng6, Federica Pisaneschi1, Pijus Mandal7, Paul G. Leonard8, Quanyu Xu,9 Qi Wu9, Yongying Jiang9, Barbara Czako10, Zhijun Kang10, John M. Asara11, Waldemar Priebe4, William Bornmann12, Joseph R. Marszalek3, Ronald A. DePinho13 and Florian L. Muller#1 1) Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX 77054 2) Institute of Stroke and Cerebrovascular Disease, The University of Texas Health Science Center at Houston, TX 77030 3) Center for Co-Clinical Trials, The University of Texas MD Anderson Cancer Center, Houston, TX 77054 4) Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77054 5) Institutional Analytics & Informatics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 6) Cardtronics, Inc., Houston, TX 77042 7) Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054 bioRxiv preprint doi: https://doi.org/10.1101/331538; this version posted May 25, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. -
Promiscuity in the Part-Phosphorylative Entner–Doudoroff Pathway of the Archaeon Sulfolobus Solfataricus
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector FEBS 30191 FEBS Letters 579 (2005) 6865–6869 Promiscuity in the part-phosphorylative Entner–Doudoroff pathway of the archaeon Sulfolobus solfataricus Henry J. Lamblea, Alex Theodossisb, Christine C. Milburnb, Garry L. Taylorb, Steven D. Bullc, David W. Hougha, Michael J. Dansona,* a Centre for Extremophile Research, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK b Centre for Biomolecular Sciences, University of St. Andrews, North Haugh, St. Andrews, Fife KY16 9ST, UK c Department of Chemistry, University of Bath, Bath BA2 7AY, UK Received 19 September 2005; revised 3 November 2005; accepted 3 November 2005 Available online 1 December 2005 Edited by Stuart Ferguson dation of both glucose and galactose, producing gluconate or Abstract The hyperthermophilic archaeon Sulfolobus solfatari- cus metabolises glucose and galactose by a ÔpromiscuousÕ non- galactonate, respectively [6]. Gluconate dehydratase then phosphorylative variant of the Entner–Doudoroff pathway, in catalyses the dehydration of gluconate to D-2-keto-3-deoxyg- which a series of enzymes have sufficient substrate promiscuity luconate (KDG) and galactonate to D-2-keto-3-deoxygalacto- to permit the metabolism of both sugars. Recently, it has been nate (KDGal) [7]. Both these compounds are cleaved by KDG proposed that the part-phosphorylative Entner–Doudoroff path- aldolase to yield pyruvate and glyceraldehyde [6]. Glyceralde- way occurs in parallel in S. solfataricus as an alternative route hyde dehydrogenase is then thought to oxidise glyceraldehyde for glucose metabolism. In this report we demonstrate, by to glycerate, which is phosphorylated by glycerate kinase to in vitro kinetic studies of D-2-keto-3-deoxygluconate (KDG) ki- give 2-phosphoglycerate. -
Structures, Functions, and Mechanisms of Filament Forming Enzymes: a Renaissance of Enzyme Filamentation
Structures, Functions, and Mechanisms of Filament Forming Enzymes: A Renaissance of Enzyme Filamentation A Review By Chad K. Park & Nancy C. Horton Department of Molecular and Cellular Biology University of Arizona Tucson, AZ 85721 N. C. Horton ([email protected], ORCID: 0000-0003-2710-8284) C. K. Park ([email protected], ORCID: 0000-0003-1089-9091) Keywords: Enzyme, Regulation, DNA binding, Nuclease, Run-On Oligomerization, self-association 1 Abstract Filament formation by non-cytoskeletal enzymes has been known for decades, yet only relatively recently has its wide-spread role in enzyme regulation and biology come to be appreciated. This comprehensive review summarizes what is known for each enzyme confirmed to form filamentous structures in vitro, and for the many that are known only to form large self-assemblies within cells. For some enzymes, studies describing both the in vitro filamentous structures and cellular self-assembly formation are also known and described. Special attention is paid to the detailed structures of each type of enzyme filament, as well as the roles the structures play in enzyme regulation and in biology. Where it is known or hypothesized, the advantages conferred by enzyme filamentation are reviewed. Finally, the similarities, differences, and comparison to the SgrAI system are also highlighted. 2 Contents INTRODUCTION…………………………………………………………..4 STRUCTURALLY CHARACTERIZED ENZYME FILAMENTS…….5 Acetyl CoA Carboxylase (ACC)……………………………………………………………………5 Phosphofructokinase (PFK)……………………………………………………………………….6 -
Coupling of Creatine Kinase to Glycolytic Enzymes at the Sarcomeric I-Band of Skeletal Muscle: a Biochemical Study in Situ
Journal of Muscle Research and Cell Motility 21: 691±703, 2000. 691 Ó 2000 Kluwer Academic Publishers. Printed in the Netherlands. Coupling of creatine kinase to glycolytic enzymes at the sarcomeric I-band of skeletal muscle: a biochemical study in situ THERESIA KRAFT2,*, T. HORNEMANN1, M. STOLZ1,à, V. NIER2, and T. WALLIMANN1 1Swiss Federal Institute of Technology, Institute of Cell Biology, ETH ZuÈrich, HoÈnggerberg, CH-8093 ZuÈrich, Switzerland; 2Medizinische Hochschule Hannover, Molekular- und Zellphysiologie, D-30625 Hannover, Germany Received 29 September 2000; accepted in revised form 3 October 2000 Abstract The speci®c interaction of muscle type creatine-kinase (MM-CK) with the myo®brillar M-line was demonstrated by exchanging endogenous MM-CK with an excess of ¯uorescently labeled MM-CK in situ, using chemically skinned skeletal muscle ®bers and confocal microscopy. No binding of labeled MM-CK was noticed at the I-band of skinned ®bers, where the enzyme is additionally located in vivo, as shown earlier by immuno¯uorescence staining of cryosections of intact muscle. However, when rhodamine-labeled MM-CK was diused into skinned ®bers that had been preincubated with phosphofructokinase (PFK), a glycolytic enzyme known to bind to actin, a striking in vivo- like interaction of Rh-MM-CK with the I-band was found, presumably mediated by binding of Rh-MM-CK to the glycolytic enzyme. Aldolase, another actin-binding glycolytic enzyme was also able to bind Rh-MM-CK to the I- band, but formation of the complex occurred preferably at long sarcomere length (>3.0 lm). Neither pyruvate kinase, although known for its binding to actin, nor phosphoglycerate kinase (PGK), not directly interacting with the I-band itself, did mediate I-band targeting of MM-CK. -
Prefoldin-Like Bud27 Influences the Transcription of Ribosomal Components and Ribosome Biogenesis in Saccharomyces Cerevisiae
Downloaded from rnajournal.cshlp.org on September 27, 2021 - Published by Cold Spring Harbor Laboratory Press Prefoldin-like Bud27 influences the transcription of ribosomal components and ribosome biogenesis in Saccharomyces cerevisiae VERÓNICA MARTÍNEZ-FERNÁNDEZ,1,7,8 ABEL CUEVAS-BERMÚDEZ,1,8 FRANCISCO GUTIÉRREZ-SANTIAGO,1,8 ANA I. GARRIDO-GODINO,1 OLGA RODRÍGUEZ-GALÁN,2,3 ANTONIO JORDÁN-PLA,4 SERGIO LOIS,5 JUAN C. TRIVIÑO,5 JESÚS DE LA CRUZ,2,3 and FRANCISCO NAVARRO1,6 1Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071, Jaén, Spain 2Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, E-41013 Seville, Spain 3Departamento de Genética, Universidad de Sevilla, E-41012 Seville, Spain 4ERI Biotecmed, Facultad de Biológicas, Universitat de València, E-46100 Burjassot, Valencia, Spain 5Sistemas Genómicos. Ronda de Guglielmo Marconi, 6, 46980 Paterna, Valencia, Spain 6Centro de Estudios Avanzados en Aceite de Oliva y Olivar, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071, Jaén, Spain ABSTRACT Understanding the functional connection that occurs for the three nuclear RNA polymerases to synthesize ribosome com- ponents during the ribosome biogenesis process has been the focal point of extensive research. To preserve correct ho- meostasis on the production of ribosomal components, cells might require the existence of proteins that target a common subunit of these RNA polymerases to impact their respective activities. This work describes how the yeast prefoldin-like Bud27 protein, which physically interacts with the Rpb5 common subunit of the three RNA polymerases, is able to mod- ulate the transcription mediated by the RNA polymerase I, likely by influencing transcription elongation, the transcription of the RNA polymerase III, and the processing of ribosomal RNA. -
Supplementary Information
Supplementary information (a) (b) Figure S1. Resistant (a) and sensitive (b) gene scores plotted against subsystems involved in cell regulation. The small circles represent the individual hits and the large circles represent the mean of each subsystem. Each individual score signifies the mean of 12 trials – three biological and four technical. The p-value was calculated as a two-tailed t-test and significance was determined using the Benjamini-Hochberg procedure; false discovery rate was selected to be 0.1. Plots constructed using Pathway Tools, Omics Dashboard. Figure S2. Connectivity map displaying the predicted functional associations between the silver-resistant gene hits; disconnected gene hits not shown. The thicknesses of the lines indicate the degree of confidence prediction for the given interaction, based on fusion, co-occurrence, experimental and co-expression data. Figure produced using STRING (version 10.5) and a medium confidence score (approximate probability) of 0.4. Figure S3. Connectivity map displaying the predicted functional associations between the silver-sensitive gene hits; disconnected gene hits not shown. The thicknesses of the lines indicate the degree of confidence prediction for the given interaction, based on fusion, co-occurrence, experimental and co-expression data. Figure produced using STRING (version 10.5) and a medium confidence score (approximate probability) of 0.4. Figure S4. Metabolic overview of the pathways in Escherichia coli. The pathways involved in silver-resistance are coloured according to respective normalized score. Each individual score represents the mean of 12 trials – three biological and four technical. Amino acid – upward pointing triangle, carbohydrate – square, proteins – diamond, purines – vertical ellipse, cofactor – downward pointing triangle, tRNA – tee, and other – circle. -
Purification of 3-Phosphoglycerate Kinase from Diverse Sources by Affinity Elution Chromatography by THEODORA FIFIS and ROBERT K
Biochem. J. (1978) 175, 311-319 311 Printed in Great Britain Purification of 3-Phosphoglycerate Kinase from Diverse Sources by Affinity Elution Chromatography By THEODORA FIFIS and ROBERT K. SCOPES Department ofBiochemistry, La Trobe University, Bundoora, Victoria 3083, Australia (Received 8 March 1978) 1. Affinity elution chromatography was used to purify phosphoglycerate kinase from a variety of sources. The choice of buffer pH for the chromatography was made according to the relative electrophoretic mobility of the enzyme from the species concerned. 2. Outlines of the methods used to isolate the enzyme from over 20 sources are presented. The enzyme was purified from the muscle tissue of a variety of mammals, fish and birds, from liver of several animals, from yeast, Escherichia coli, and plant leaves. The more acidic varieties of the enzymes were purified by conventional gradient elution from ion-exchangers as affinity elution procedures were not applicable. 3. The structural and kinetic parameters investigated show that phosphoglycerate kinase is evolutionarily a highly conservative enzyme; there were few differences in properties regardless of source or function (glycolytic, gluconeogenic or photosynthetic). 4. A detailed comparison of the enzyme preparations purified from bovine muscle and bovine liver failed to detect any significant differences between them; the evidence indicates that they are genetically identical. Phosphoglycerate kinase (ATP-3-phospho-D- varies between the enzyme from one species and glycerate 1-phosphotransferase, -
Carbon Partitioning in Green Algae (Chlorophyta) and the Enolase Enzyme
Metabolites 2014, 4, 612-628; doi:10.3390/metabo403000x OPEN ACCESS metabolites ISSN 2218-1989 www.mdpi.com/journal/metabolites/ Article Carbon Partitioning in Green Algae (Chlorophyta) and the Enolase Enzyme Jürgen E. W. Polle 1,2,*, Peter Neofotis 1,2, Andy Huang 1, William Chang 1, Kiran Sury 1 and Eliza M. Wiech 1 1 Department of Biology, Brooklyn College of the City University of New York, 2900 Bedford Avenue 200NE, Brooklyn, NY 11210, USA; E-Mails: [email protected] (P.N.); [email protected] (A.H.); [email protected] (W.C.); [email protected] (K.S.); [email protected] (E.M.W.) 2 The Graduate Center of the City University of New York, 2900 Bedford Avenue 200NE, Brooklyn, NY 11210, USA * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +1-718-951-5000; Fax: +1-718-951-4659. Received: 13 June 2014; in revised form: 25 July 2014 / Accepted: 28 July 2014 / Published: 4 August 2014 Abstract: The exact mechanisms underlying the distribution of fixed carbon within photoautotrophic cells, also referred to as carbon partitioning, and the subcellular localization of many enzymes involved in carbon metabolism are still unknown. In contrast to the majority of investigated green algae, higher plants have multiple isoforms of the glycolytic enolase enzyme, which are differentially regulated in higher plants. Here we report on the number of gene copies coding for the enolase in several genomes of species spanning the major classes of green algae. Our genomic analysis of several green algae revealed the presence of only one gene coding for a glycolytic enolase [EC 4.2.1.11]. -
Functional and Physiological Discovery in the Mannonate Dehydratase Subgroup of the Enolase Superfamily
FUNCTIONAL AND PHYSIOLOGICAL DISCOVERY IN THE MANNONATE DEHYDRATASE SUBGROUP OF THE ENOLASE SUPERFAMILY BY DANIEL JOSEPH WICHELECKI DISSERTATION Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biochemistry in the Graduate College of the University of Illinois at Urbana-Champaign, 2014 Urbana, Illinois Doctoral Committee: Professor John Gerlt, Chair Professor John Cronan Professor Scott Silverman Professor Wilfred van der Donk ABSTRACT In the current post-genomic world, the exponential amassing of protein sequences is overwhelming the scientific community’s ability to experimentally assign each protein’s function. The use of automated, homology-based annotations has allowed a reprieve from this efflux of data, but has led to widespread misannotation and nonannotation in protein sequence databases. This dissertation details the functional and physiological characterization of the mannonate dehydratase subgroup (ManD) of the enolase superfamily (ENS). The outcome affirms the dangers of homology-based annotations while discovering novel metabolic pathways. Furthermore, the experimental verification of these pathways ( in vitro and in vivo ) has provided a platform to test the general strategies for improved functional and metabolic characterization being developed by the Enzyme Function Initiative (EFI). Prior to this study, one member of the ManD subgroup had been characterized and was shown to dehydrate D-mannonate to 2-keto-3-deoxy-D-gluconate. Forty-two additional members of the ManD, selected from across the sequence space of the subgroup, were screened for activity and kinetic constants were determined. The members of the once isofunctional subgroup were found to differ in both catalytic efficiency and substrate specificity: 1) high 3 4 -1 -1 efficiency (k cat /K M = 10 to 10 M s ) dehydration of D-mannonate, 2) low efficiency (k cat /K M = 10 1 to 10 2 M-1s-1) dehydration of D-mannonate and/or D-gluconate, and 3) no-activity with either D-mannonate or D-gluconate (or any other acid sugar tested). -
Downregulation of Phosphoglycerate Kinase 1 by Shrna Sensitizes U251 Xenografts to Radiotherapy
ONCOLOGY REPORTS 32: 1513-1520, 2014 Downregulation of phosphoglycerate kinase 1 by shRNA sensitizes U251 xenografts to radiotherapy YI-JUN CHENG1, HAO DING1, HUA-QING DU2, Hua YAN1, JIN-BING ZHAO1, WEN-BIN ZHANG1, YUAN-JIE ZOU1, HONG-YI LIU1 and HONG XIAO2 1Department of Neurosurgery and 2Neuro-Psychiatric Institute, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, Jiangsu, P.R. China Received April 6, 2014; Accepted July 9, 2014 DOI: 10.3892/or.2014.3353 Abstract. Phosphoglycerate kinase 1 (PGK1) has been demon- radiotherapy is one of the standard treatments for glioma. Yet, strated to be involved in radioresistance. The present study was the prognosis remains dismal due to the ability of gliomas to designed to investigate the effect of PGK1 on the radioresis- infiltrate diffusely into the normal brain parenchyma, a direct tance in vivo. U251 glioma cells were transfected with the short consequence of the transformation into genetic higher-grade hairpin RNA (shRNA)-PGK1 and pcDNA3.1-PGK1 using gliomas and recurrence (4-6). As known, radioresistance is Lipofectamine 2000. The radiosensitivity of U251 xenografts a common phenomenon in gliomas and, to date there are no was observed by tumor growth curve following radiotherapy. valid biomarkers for evaluating radiosensitivity. Quantitative PCR, western blot analysis and immunohisto- In fact, radiotherapy which relies on the generation of chemistry were performed to evaluate PGK1 expression in the oxygen super-radicals, often fails to kill tumor cells, due to xenografts from the different tumor models. The expression inadequate oxygen stress within the tumor cell mass (7,8). of PGK1 was maximally inhibited in response to shRNA4 at However, in tumor microenvironments where oxygen is scarce 24 h after the transfection in vitro. -
19F NMR Measurements of the Rotational Mobility of Proteins in Vivo
490 Biophysical Journal Volume 72 January 1997 490-498 19F NMR Measurements of the Rotational Mobility of Proteins In Vivo Simon-Peter Williams, Peter M. Haggie, and Kevin M. Brindle Department of Biochemistry, University of Cambridge, Cambridge CB2 1 QW, United Kingdom ABSTRACT Three glycolytic enzymes, hexokinase, phosphoglycerate kinase, and pyruvate kinase, were fluorine labeled in the yeast Saccharomyces cerevisiae by biosynthetic incorporation of 5-fluorotryptophan. 19F NMR longitudinal relaxation time measurements on the labeled enzymes were used to assess their rotational mobility in the intact cell. Comparison with the results obtained from relaxation time measurements of the purified enzymes in vitro and from theoretical calculations showed that two of the labeled enzymes, phosphoglycerate kinase and hexokinase, were tumbling in a cytoplasm that had a viscosity approximately twice that of water. There were no detectable signals from pyruvate kinase in vivo, although it could be detected in diluted cell extracts, indicating that there was some degree of motional restriction of the enzyme in the intact cell. INTRODUCTION Studies of the kinetic properties of enzymes in vitro can Brooks and Storey, 1991a,b; Wu et al., 1991). However, give important information on the possible roles of these fluorescence microscopy measurements on fibroblasts, mi- enzymes in the control of metabolism in vivo. This ap- croinjected with fluorescently tagged glycolytic enzymes, proach presumes, however, a detailed knowledge of their have demonstrated -
Name: Chem 465 Biochemistry II Test 1 Spring 2019 Multiple Choice (4 Points Apiece): 1. in an Anaerobic Muscle Preparation, Lact
Name: Chem 465 Biochemistry II Test 1 Spring 2019 Multiple choice (4 points apiece): 1. In an anaerobic muscle preparation, lactate formed from glucose labeled in C-3 and C-4 would be labeled in: A) all three carbon atoms. B) only the carbon atom carrying the OH. C) only the carboxyl carbon atom. D) only the methyl carbon atom. E) the methyl and carboxyl carbon atoms. 2. In an anaerobic muscle preparation, lactate formed from glucose labeled in C-2 would be labeled in: A) all three carbon atoms. B) only the carbon atom carrying the OH. C) only the carboxyl carbon atom. D) only the methyl carbon atom. E) the methyl and carboxyl carbon atoms. 3. All of the following enzymes involved in the flow of carbon from glucose to lactate (glycolysis) are also involved in the reversal of this flow (gluconeogenesis) except: A) 3-phosphoglycerate kinase. B) aldolase. C) enolase. D) phosphofructokinase-1. E) phosphoglucoisomerase. 4. Cellular isozymes of pyruvate kinase are allosterically inhibited by: A) high concentrations of AMP. B) high concentrations of ATP. C) high concentrations of citrate. D) low concentrations of acetyl-CoA. E) low concentrations of ATP. 5. Which of the following is not true of the reaction catalyzed by the pyruvate dehydrogenase complex? A) Biotin participates in the decarboxylation. B) Both NAD+ and a flavin nucleotide act as electron carriers. C) The reaction occurs in the mitochondrial matrix. D) The substrate is held by the lipoyl-lysine "swinging arm." E) Two different cofactors containing -SH groups participate. 6. (20 points) This page is blank because I want you to fill it in with the glycolytic pathway from glucose to pyruvate showing the structure of all intermediates.