Drosophila Larvae Synthesize the Putative Oncometabolite L-2-Hydroxyglutarate During Normal Developmental Growth

Total Page:16

File Type:pdf, Size:1020Kb

Drosophila Larvae Synthesize the Putative Oncometabolite L-2-Hydroxyglutarate During Normal Developmental Growth Drosophila larvae synthesize the putative oncometabolite L-2-hydroxyglutarate during normal developmental growth Hongde Lia, Geetanjali Chawlaa, Alexander J. Hurlburta, Maria C. Sterretta, Olga Zaslaverb, James Coxc, Jonathan A. Kartyd, Adam P. Rosebrockb,e, Amy A. Caudyb,e, and Jason M. Tennessena,1 aDepartment of Biology, Indiana University, Bloomington, IN 47405; bDepartment of Molecular Genetics, University of Toronto, Toronto, ON, Canada M5S 3E1; cDepartment of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112; dDepartment of Chemistry, Indiana University, Bloomington, IN 47405; and eDonnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada M5S 3E1 Edited by Jasper Rine, University of California, Berkeley, CA, and approved December 23, 2016 (received for review August 23, 2016) L-2-hydroxyglutarate (L-2HG) has emerged as a putative oncome- neomorphic mutations in the active site of isocitrate dehydrogenase tabolite that is capable of inhibiting enzymes involved in metab- 1 or 2 (IDH1/2) (5). Tumors that harbor these IDH1/2 mutations olism, chromatin modification, and cell differentiation. However, inappropriately convert 2-oxoglutarate (2OG) to D-2HG, which acts despite the ability of L-2HG to interfere with a broad range of as a competitive inhibitor of 2-oxoglutarate–dependent dioxygenases cellular processes, this molecule is often characterized as a [2OGDs; e.g., Jmj histone lysine demethylases, ten-eleven trans- metabolic waste product. Here, we demonstrate that Drosophila location (TET) enzyme family] (3, 6–9). As a result, IDH1/2 mutant larvae use the metabolic conditions established by aerobic glycol- cells experience widespread chromatin remodeling and changes in ysis to both synthesize and accumulate high concentrations of gene expression and are unable to differentiate properly (8, 9). L-2HG during normal developmental growth. A majority of the Although most oncometabolite research is focused on D-2HG, larval L-2HG pool is derived from glucose and dependent on the the L-2-hydroxyglutarate (L-2HG) enantiomer is an even more Drosophila estrogen-related receptor (dERR), which promotes potent 2OGD inhibitor, and high L-2HG levels are associated L-2HG synthesis by up-regulating expression of the Drosophila with renal cell carcinomas, gliomas, and a neurometabolic dis- homolog of lactate dehydrogenase (dLdh). We also show that order known as L-2-hydroxyglutaric aciduria (10–12). Unlike dLDH is both necessary and sufficient for directly synthesizing D-2HG, however, L-2HG has no known role in metabolism and L-2HG and the Drosophila homolog of L-2-hydroxyglutarate dehy- eukaryotes lack an enzyme dedicated to L-2HG synthesis. In- drogenase (dL2HGDH), which encodes the enzyme that breaks stead, L-2HG is considered an aberrant metabolite produced by down L-2HG, is required for stage-specific degradation of the the nonspecific activity of enzymes such as malate dehydrogenase, L-2HG pool. In addition, dLDH also indirectly promotes L-2HG accu- lactate dehydrogenase A (LDHA), and lactate dehydrogenase C mulation via synthesis of lactate, which activates a metabolic feed- (12–18). Consistent with these observations, L-2HG accumula- GENETICS forward mechanism that inhibits dL2HGDH activity and stabilizes tion in cancer cells does not result from ectopic synthesis; rather, L-2HG levels. Finally, we use a genetic approach to demonstrate it stems from decreased expression of the enzyme L-2-hydrox- that dLDH and L-2HG influence position effect variegation and yglutarate dehydrogenase (L2HGDH), which is solely responsible DNA methylation, suggesting that this compound serves to coor- dinate glycolytic flux with epigenetic modifications. Overall, our for L-2HG degradation (10, 19). Therefore, most studies suggest studies demonstrate that growing animal tissues synthesize L-2HG that neither healthy tissues nor cancer cells appear capable of in a controlled manner, reveal a mechanism that coordinates glu- regulating L-2HG production. This model of L-2HG synthesis, cose catabolism with L-2HG synthesis, and establish the fly as a however, has been challenged by a recent study of T lymphocytes, unique model system for studying the endogenous functions of L-2HG during cell growth and proliferation. Significance 2-hydroxyglutarate | LDH | lactate | Warburg effect | Oncometabolites are small molecules that promote tumor for- estrogen-related receptor mation and growth. L-2-hydroxyglutarate (L-2HG) is a putative oncometabolite that is associated with gliomas and renal cell ne of the hallmarks of cancer is a dramatic reprograming of carcinomas, as well as a severe neurometabolic disorder known Ocellular metabolism that results in enhanced biosynthesis as L-2-hydroxyglutaric aciduria. However, despite that L-2HG is (1). These metabolic changes are particularly apparent in tumors commonly considered a metabolic waste product, this com- that use the Warburg effect, also referred to as aerobic glycolysis, pound was recently discovered to control immune cell fate, a metabolic program characterized by elevated levels of glucose thereby demonstrating that it has endogenous functions in consumption and enhanced lactate production (1, 2). By activating healthy animal cells. Here, we find that the fruit fly, Drosophila aerobic glycolysis, tumors are able to synthesize macromolecules melanogaster, also synthesizes high concentrations of L-2HG rapidly from glycolytic intermediates. In addition, elevated levels during normal larval growth. Our discovery establishes the fly of lactate dehydrogenase (LDH) activity allow proliferating cells as a genetic model for studying this putative oncometabolite in + to synthesize lactate and maintain the NAD levels required for healthy animal tissues. high rates of glucose catabolism and biomass production (1). Author contributions: H.L., G.C., A.A.C., and J.M.T. designed research; H.L., G.C., A.J.H., The metabolic reprogramming of cancer cells, however, extends M.C.S., J.C., J.A.K., and J.M.T. performed research; H.L., G.C., O.Z., A.P.R., A.A.C., and J.M.T. beyond biosynthesis, as many tumors also generate progrowth contributed new reagents/analytic tools; H.L., G.C., A.J.H., M.C.S., J.C., and J.M.T. analyzed metabolites, or oncometabolites, that promote tumor formation data; and H.L. and J.M.T. wrote the paper. via nonmetabolic means. Most notable among these compounds The authors declare no conflict of interest. is D-2-hydroxyglutarate (D-2HG), which is associated with cancers This article is a PNAS Direct Submission. such as gliomas and acute myelogenous leukemias (3). Although 1To whom correspondence should be addressed. Email: [email protected]. γ D-2HG is generated as a normal byproduct of -hydroxybutyrate This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. metabolism (4), oncogenic D-2HG production is the result of 1073/pnas.1614102114/-/DCSupplemental. www.pnas.org/cgi/doi/10.1073/pnas.1614102114 PNAS | February 7, 2017 | vol. 114 | no. 6 | 1353–1358 Downloaded by guest on September 25, 2021 which revealed that these immune cells generate L-2HG as a A Drosophila development B L2 larvae means of controlling cell fate and gene expression (20). Fur- Emb Larva wpp Adult thermore, both hypoxia and the disruption of mitochondrial 2 metabolism cause human cells to generate high levels of L-2HG, 100 indicating that synthesis of this compound might alleviate oxi- dative stress (17, 21–23). These observations hint at diverse en- 1 dogenous roles for L-2HG and suggest that the function of this 50 putative oncometabolite should be further studied in healthy 2HG (nmol/mg) tissues. To address this need, we have established the fruit fly Relative [2HG] 0 0 Drosophila melanogaster as a genetic model system for studying 1820317654 9 L- D- L-2HG in the context of aerobic glycolysis and rapid tissue growth. Staged Timepoint (see legend) The fly is ideally suited to study the molecular mechanisms that link glycolytic flux to biosynthesis. Similar to cancer cells, growing C Kc167 BG1-c1 D L2 larvae Drosophila larvae up-regulate glycolysis, the pentose phosphate 1 1 U-13C-glucose pathway, and lactate production as means of supporting the nearly 0.8 0.8 U-13C-proline 200-fold increase in body mass that occurs during this develop- mental stage (24). The resulting metabolic program exhibits the 0.6 0.6 hallmark characteristics of aerobic glycolysis and establishes the 0.4 0.4 fly as a powerful in vivo model for studying this metabolic state. 0.2 Furthermore, studies in the fly were the first to demonstrate that 0.2 2HG (nmol/mg) 0 the estrogen-related receptor (ERR) family of nuclear receptors Fraction of labelled 2HG 0 acts as a conserved transcriptional regulator of aerobic glycolysis L- D- L- D- 0 5 15 25 (24–26). Here, we extend the metabolic parallels between Dro- Time (hours) sophila development and tumor growth by demonstrating that Fig. 1. Drosophila larvae accumulate high concentrations of L-2HG. (A) Relative the Drosophila estrogen-related receptor (dERR) also promotes abundance of 2HG in a w1118 background. Staged time points are as follows: L-2HG synthesis. Moreover, we determine that the larval L-2HG (1) embryos (Emb; 0–12 h after egg laying), (2) Emb (12–24 h after egg laying), pool is largely derived from glucose oxidation and synthesized (3) L1 larvae, (4) L2 larvae, (5) early-L3 larvae (0–12 h after L2-L3 molt), (6) mid-L3 by the Drosophila ortholog of LDH (dLDH), thereby establishing larvae (24–36 h after L2-L3 molt), (7) wandering L3 larvae, (8) white prepupae a direct link between larval glycolytic metabolism and L-2HG (wpp), (9) adult females (3 d posteclosion), and (10) adult males (3 d posteclosion). production. Finally, we demonstrate that dLDH and L-2HG are Data are represented as box plots (n = 6). The concentrations of D-2HG and L-2HG key regulators of position effect variegation (PEV) and DNA in midsecond-instar w1118 larvae (B)andtheDrosophila cell lines Kc167 and BG1-c1 (C) are shown.
Recommended publications
  • The Self-Inhibitory Nature of Metabolic Networks and Its Alleviation Through Compartmentalization
    ARTICLE Received 30 Oct 2016 | Accepted 23 May 2017 | Published 10 Jul 2017 DOI: 10.1038/ncomms16018 OPEN The self-inhibitory nature of metabolic networks and its alleviation through compartmentalization Mohammad Tauqeer Alam1,2, Viridiana Olin-Sandoval1,3, Anna Stincone1,w, Markus A. Keller1,4, Aleksej Zelezniak1,5,6, Ben F. Luisi1 & Markus Ralser1,5 Metabolites can inhibit the enzymes that generate them. To explore the general nature of metabolic self-inhibition, we surveyed enzymological data accrued from a century of experimentation and generated a genome-scale enzyme-inhibition network. Enzyme inhibition is often driven by essential metabolites, affects the majority of biochemical processes, and is executed by a structured network whose topological organization is reflecting chemical similarities that exist between metabolites. Most inhibitory interactions are competitive, emerge in the close neighbourhood of the inhibited enzymes, and result from structural similarities between substrate and inhibitors. Structural constraints also explain one-third of allosteric inhibitors, a finding rationalized by crystallographic analysis of allosterically inhibited L-lactate dehydrogenase. Our findings suggest that the primary cause of metabolic enzyme inhibition is not the evolution of regulatory metabolite–enzyme interactions, but a finite structural diversity prevalent within the metabolome. In eukaryotes, compartmentalization minimizes inevitable enzyme inhibition and alleviates constraints that self-inhibition places on metabolism. 1 Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK. 2 Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK. 3 Department of Food Science and Technology, Instituto Nacional de Ciencias Me´dicas y Nutricio´n Salvador Zubira´n, Vasco de Quiroga 15, Tlalpan, 14080 Mexico City, Mexico.
    [Show full text]
  • Identification and Characterization of TPRKB Dependency in TP53 Deficient Cancers
    Identification and Characterization of TPRKB Dependency in TP53 Deficient Cancers. by Kelly Kennaley A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Molecular and Cellular Pathology) in the University of Michigan 2019 Doctoral Committee: Associate Professor Zaneta Nikolovska-Coleska, Co-Chair Adjunct Associate Professor Scott A. Tomlins, Co-Chair Associate Professor Eric R. Fearon Associate Professor Alexey I. Nesvizhskii Kelly R. Kennaley [email protected] ORCID iD: 0000-0003-2439-9020 © Kelly R. Kennaley 2019 Acknowledgements I have immeasurable gratitude for the unwavering support and guidance I received throughout my dissertation. First and foremost, I would like to thank my thesis advisor and mentor Dr. Scott Tomlins for entrusting me with a challenging, interesting, and impactful project. He taught me how to drive a project forward through set-backs, ask the important questions, and always consider the impact of my work. I’m truly appreciative for his commitment to ensuring that I would get the most from my graduate education. I am also grateful to the many members of the Tomlins lab that made it the supportive, collaborative, and educational environment that it was. I would like to give special thanks to those I’ve worked closely with on this project, particularly Dr. Moloy Goswami for his mentorship, Lei Lucy Wang, Dr. Sumin Han, and undergraduate students Bhavneet Singh, Travis Weiss, and Myles Barlow. I am also grateful for the support of my thesis committee, Dr. Eric Fearon, Dr. Alexey Nesvizhskii, and my co-mentor Dr. Zaneta Nikolovska-Coleska, who have offered guidance and critical evaluation since project inception.
    [Show full text]
  • A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
    Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated.
    [Show full text]
  • Thiamin Biofortification of Crops
    Thiamin biofortification of crops Aymeric Goyera,b a Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97330, United States of America b Hermiston Agricultural Research and Extension Center, Oregon State University, Hermiston, OR 97838, United States of America Corresponding author: Aymeric Goyer [email protected] 1 Abstract Thiamin is essential for human health. While plants are the ultimate source of thiamin in most human diets, staple foods like white rice have low thiamin content. Therefore, populations whose diets are mainly based on low-thiamin staple crops suffer from thiamin deficiency. Biofortification of rice grain by engineering the thiamin biosynthesis pathway has recently been attempted, with up to fivefold increase in thiamin content in unpolished seeds. However, polished seeds that retain only the starchy endosperm had similar thiamin content than that of non-engineered plants. Various factors such as limited supply of precursors, limited activity of thiamin biosynthetic enzymes, dependence on maternal tissues to supply thiamin, or lack of thiamin stabilizing proteins may have hindered thiamin increase in the endosperm. Introduction Thiamin (vitamin B1), in its diphosphate form (ThDP), functions as a cofactor for key enzymes of carbohydrates and amino acid metabolism in all living organisms [1,2]. While plants, fungi and bacteria can synthesize thiamin de novo, humans cannot and must obtain it from food. Although plant foods are a major source of thiamin, some staple crops like rice contain relatively low amounts of thiamin. Industrialized milling of the rice grain that removes the outer layers of the seed, i.e. the pericarp, testa, nucellus, and aleurone layer, as well as the embryo (Figure 1), further depletes the grain’s thiamin content [3].
    [Show full text]
  • Teleological Role of L-2-Hydroxyglutarate
    © 2020. Published by The Company of Biologists Ltd | Disease Models & Mechanisms (2020) 13, dmm045898. doi:10.1242/dmm.045898 RESEARCH ARTICLE Teleological role of L-2-hydroxyglutarate dehydrogenase in the kidney Garrett Brinkley1, Hyeyoung Nam1, Eunhee Shim1,*, Richard Kirkman1, Anirban Kundu1, Suman Karki1, Yasaman Heidarian2, Jason M. Tennessen2, Juan Liu3, Jason W. Locasale3, Tao Guo4, Shi Wei4, Jennifer Gordetsky5, Teresa L. Johnson-Pais6, Devin Absher7, Dinesh Rakheja8, Anil K. Challa9 and Sunil Sudarshan1,10,‡ ABSTRACT insight into the physiological role of L2HGDH as well as mechanisms L-2-hydroxyglutarate (L-2HG) is an oncometabolite found elevated in that promote L-2HG accumulation in disease states. renal tumors. However, this molecule might have physiological roles that extend beyond its association with cancer, as L-2HG levels are KEY WORDS: L-2-hydroxyglutarate, L-2-hydroxyglutarate dehydrogenase, TCA cycle, PPARGC1A elevated in response to hypoxia and during Drosophila larval development. L-2HG is known to be metabolized by L-2HG dehydrogenase (L2HGDH), and loss of L2HGDH leads to elevated INTRODUCTION L-2HG levels. Despite L2HGDH being highly expressed in the kidney, Oncometabolites are small molecules that have been found elevated its role in renal metabolism has not been explored. Here, we report our in various malignancies. To date, these molecules include the findings utilizing a novel CRISPR/Cas9 murine knockout model, with tricarboxylic acid (TCA) cycle intermediates succinate and fumarate a specific focus on the role of L2HGDH in the kidney. Histologically, as well as both enantiomers of 2-hydroxyglutarate (D-2HG and L2hgdh knockout kidneys have no demonstrable histologic L-2HG) (Tomlinson et al., 2002; Baysal et al., 2000; Niemann and abnormalities.
    [Show full text]
  • Enzyme DHRS7
    Toward the identification of a function of the “orphan” enzyme DHRS7 Inauguraldissertation zur Erlangung der Würde eines Doktors der Philosophie vorgelegt der Philosophisch-Naturwissenschaftlichen Fakultät der Universität Basel von Selene Araya, aus Lugano, Tessin Basel, 2018 Originaldokument gespeichert auf dem Dokumentenserver der Universität Basel edoc.unibas.ch Genehmigt von der Philosophisch-Naturwissenschaftlichen Fakultät auf Antrag von Prof. Dr. Alex Odermatt (Fakultätsverantwortlicher) und Prof. Dr. Michael Arand (Korreferent) Basel, den 26.6.2018 ________________________ Dekan Prof. Dr. Martin Spiess I. List of Abbreviations 3α/βAdiol 3α/β-Androstanediol (5α-Androstane-3α/β,17β-diol) 3α/βHSD 3α/β-hydroxysteroid dehydrogenase 17β-HSD 17β-Hydroxysteroid Dehydrogenase 17αOHProg 17α-Hydroxyprogesterone 20α/βOHProg 20α/β-Hydroxyprogesterone 17α,20α/βdiOHProg 20α/βdihydroxyprogesterone ADT Androgen deprivation therapy ANOVA Analysis of variance AR Androgen Receptor AKR Aldo-Keto Reductase ATCC American Type Culture Collection CAM Cell Adhesion Molecule CYP Cytochrome P450 CBR1 Carbonyl reductase 1 CRPC Castration resistant prostate cancer Ct-value Cycle threshold-value DHRS7 (B/C) Dehydrogenase/Reductase Short Chain Dehydrogenase Family Member 7 (B/C) DHEA Dehydroepiandrosterone DHP Dehydroprogesterone DHT 5α-Dihydrotestosterone DMEM Dulbecco's Modified Eagle's Medium DMSO Dimethyl Sulfoxide DTT Dithiothreitol E1 Estrone E2 Estradiol ECM Extracellular Membrane EDTA Ethylenediaminetetraacetic acid EMT Epithelial-mesenchymal transition ER Endoplasmic Reticulum ERα/β Estrogen Receptor α/β FBS Fetal Bovine Serum 3 FDR False discovery rate FGF Fibroblast growth factor HEPES 4-(2-Hydroxyethyl)-1-Piperazineethanesulfonic Acid HMDB Human Metabolome Database HPLC High Performance Liquid Chromatography HSD Hydroxysteroid Dehydrogenase IC50 Half-Maximal Inhibitory Concentration LNCaP Lymph node carcinoma of the prostate mRNA Messenger Ribonucleic Acid n.d.
    [Show full text]
  • Supplementary Materials
    Supplementary Materials COMPARATIVE ANALYSIS OF THE TRANSCRIPTOME, PROTEOME AND miRNA PROFILE OF KUPFFER CELLS AND MONOCYTES Andrey Elchaninov1,3*, Anastasiya Lokhonina1,3, Maria Nikitina2, Polina Vishnyakova1,3, Andrey Makarov1, Irina Arutyunyan1, Anastasiya Poltavets1, Evgeniya Kananykhina2, Sergey Kovalchuk4, Evgeny Karpulevich5,6, Galina Bolshakova2, Gennady Sukhikh1, Timur Fatkhudinov2,3 1 Laboratory of Regenerative Medicine, National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov of Ministry of Healthcare of Russian Federation, Moscow, Russia 2 Laboratory of Growth and Development, Scientific Research Institute of Human Morphology, Moscow, Russia 3 Histology Department, Medical Institute, Peoples' Friendship University of Russia, Moscow, Russia 4 Laboratory of Bioinformatic methods for Combinatorial Chemistry and Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia 5 Information Systems Department, Ivannikov Institute for System Programming of the Russian Academy of Sciences, Moscow, Russia 6 Genome Engineering Laboratory, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia Figure S1. Flow cytometry analysis of unsorted blood sample. Representative forward, side scattering and histogram are shown. The proportions of negative cells were determined in relation to the isotype controls. The percentages of positive cells are indicated. The blue curve corresponds to the isotype control. Figure S2. Flow cytometry analysis of unsorted liver stromal cells. Representative forward, side scattering and histogram are shown. The proportions of negative cells were determined in relation to the isotype controls. The percentages of positive cells are indicated. The blue curve corresponds to the isotype control. Figure S3. MiRNAs expression analysis in monocytes and Kupffer cells. Full-length of heatmaps are presented.
    [Show full text]
  • Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
    Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase
    [Show full text]
  • Characterization of the Heterooligomeric Red-Type Rubisco Activase from Red Algae
    Characterization of the heterooligomeric red-type rubisco activase from red algae Nitin Loganathana, Yi-Chin Candace Tsaia, and Oliver Mueller-Cajara,1 aSchool of Biological Sciences, Nanyang Technological University, Singapore 637551 Edited by Sue Wickner, National Cancer Institute, National Institutes of Health, Bethesda, MD, and approved October 28, 2016 (received for review July 2, 2016) The photosynthetic CO2-fixing enzyme ribulose 1,5-bisphosphate car- Three distantly related classes of Rcas (green, red, and CbbQO boxylase/oxygenase (rubisco) is inhibited by nonproductive binding types) have been identified so far (13–16). They all belong to the + of its substrate ribulose-1,5-bisphosphate (RuBP) and other sugar superfamily of AAA (ATPases associated with various cellular phosphates. Reactivation requires ATP-hydrolysis–powered remodel- activities) proteins (17) and function as ring-shaped hexamers that ing of the inhibited complexes by diverse molecular chaperones couple the energy of ATP hydrolysis to rubisco remodeling. known as rubisco activases (Rcas). Eukaryotic phytoplankton of the CbbQO requires one adaptor protein CbbO to associate with the red plastid lineage contain so-called red-type rubiscos, some of which AAA hexamer CbbQ6 to function (15). Common themes in the have been shown to possess superior kinetic properties to green-type activation mechanism are emerging (such as manipulation of rubiscos found in higher plants. These organisms are known to en- the large subunit C terminus for red-type Rca and CbbQO), al- code multiple homologs of CbbX, the α-proteobacterial red-type acti- though clear differences are also apparent (3, 12, 15). vase. Here we show that the gene products of two cbbX genes Following the primary endosymbiotic event, the green plastid encoded by the nuclear and plastid genomes of the red algae lineage toward green algae and plants retained the green-type form Cyanidioschyzon merolae are nonfunctional in isolation, but together IB rubisco from the cyanobacterial ancestor.
    [Show full text]
  • Bacterial Microcompartments: Catalysis- Enhancing Metabolic Modules for Next Generation Metabolic and Biomedical Engineering Henning Kirst1,2 and Cheryl A
    Kirst and Kerfeld BMC Biology (2019) 17:79 https://doi.org/10.1186/s12915-019-0691-z QUESTION AND ANSWER Open Access Bacterial microcompartments: catalysis- enhancing metabolic modules for next generation metabolic and biomedical engineering Henning Kirst1,2 and Cheryl A. Kerfeld1,2,3* Abstract What defines the BMC shell? BMCs are defined by the structural proteins that compose Bacterial cells have long been thought to be simple their “membranes”. There are three structural groups of cells with little spatial organization, but recent research shell proteins: BMC-H (Pfam00936), which form hex- has shown that they exhibit a remarkable degree of agonal hexamers [1]; BMC-P (Pfam03319), which from subcellular differentiation. Indeed, bacteria even have pentagonal pentamers [7, 8], and BMC-T (a tandem fu- organelles such as magnetosomes for sensing magnetic sion of the Pfam00936), which subdivide into two types: fields or gas vesicles controlling cell buoyancy. trimers (BMC-TS)[9–12], and stacked dimers of trimers A functionally diverse group of bacterial organelles (BMC-TD)(Fig.1a) [13–15]. Pores, typically at the cyclic are the bacterial microcompartments (BMCs) that axis of symmetry in the hexamers, vary in size (4–7Å in fulfill specialized metabolic needs. Modification and diameter) and charge, thereby contributing to selective reengineering of these BMCs enable innovative permeability (Fig. 1a) [1, 13–19]. It has been shown that approaches for metabolic engineering and some BMC-H proteins are specifically permeable to an- − D nanomedicine. ions like HCO3 [20]. The BMC-T trimers can have gated pores, meaning they have an open and closed con- formation (closed conformation shown in Fig.
    [Show full text]
  • Features and Further Application Related to L2HGA
    月 17, 2018 17:30 CST Features and Further Application Related to L2HGA L-2-hydroxyglutarate dehydrogenase is a mitochondrial enzyme in humans that is encoded by the L2HGDH gene on chromosome 14. This protein is a spotlight for research because of its clinical significance. Mutations in the L2HGDH gene cause L-2-hydroxyglutaric aciduria, which is a rare autosomal recessive neuro-metabolic disorder. Toxic accumulation of high concentration of L-2-hydroxyglutaric acid in the plasma and cerebrospinal fluid are discovered in individuals with L2HGDH mutations. Moreover, the researcher has discovered that patients with L-2- hydroxyglutaric aciduria (L2HGA) also present neurological symptoms and characteristic neuro-radiological findings, especially subcortical white matter abnormalities. After adopting the genotype-first approach of the whole exome sequence, compound heterozygous mutations of L2HGDH was discovered. The sample investigated was an adult patient with intellectual disability and epilepsy. A retrospective assay was also used to prove the concentrations of 2-hydroxyglutaric acid in the urine did increase. These findings taken together indicated that neuro-radiological findings of subcortical white matter abnormalities are features of L2HGA(the disease caused by abnormality in L2HGDH), moreover, clinical exome sequencing plays a role in compensating for gene expression clinical evaluations. Researcher also studied that whether L-2-HGA could provoke DNA oxidative damage in blood leukocytes and whether L-carnitine (LC) could prevent this kind of in vitro DNA damage. Researcher discovered that a certain amount (30 μM) of L-2-HG significantly induced DNA damage. However, this kind of damage is effectively prevented by 30 and 150 μM of LC.
    [Show full text]
  • Coupling Between D-3-Phosphoglycerate Dehydrogenase and D-2-Hydroxyglutarate Dehydrogenase Drives Bacterial L-Serine Synthesis
    PNAS PLUS Coupling between D-3-phosphoglycerate dehydrogenase and D-2-hydroxyglutarate dehydrogenase drives bacterial L-serine synthesis Wen Zhanga,b, Manman Zhanga, Chao Gaoa,1, Yipeng Zhanga, Yongsheng Gea, Shiting Guoa, Xiaoting Guoa, Zikang Zhouc, Qiuyuan Liua, Yingxin Zhanga, Cuiqing Maa, Fei Taoc, and Ping Xuc,1 aState Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, People’s Republic of China; bCenter for Gene and Immunotherapy, The Second Hospital of Shandong University, Jinan 250033, People’s Republic of China; and cState Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China Edited by Joshua D. Rabinowitz, Princeton University, Princeton, NJ, and accepted by Editorial Board Member Gregory A. Petsko July 26, 2017 (receivedfor review November 17, 2016) L-Serine biosynthesis, a crucial metabolic process in most domains Certain enzymes exhibit, beyond their classical functions, 2-KG– of life, is initiated by D-3-phosphoglycerate (D-3-PG) dehydrogena- reducing activity for D-2-HG production. These enzymes include tion, a thermodynamically unfavorable reaction catalyzed by D-3-PG hydroxyacid-oxoacid transhydrogenase (HOT) in H. sapiens (20, dehydrogenase (SerA). D-2-Hydroxyglutarate (D-2-HG) is traditionally 21), 4-phospho-D-erythronate dehydrogenase (PdxB) in E. coli (22), viewed as an abnormal metabolite associated with cancer and UDP-N-acetyl-2-amino-2-deoxyglucuronate dehydrogenase (WbpB) neurometabolic disorders. Here, we reveal that bacterial anabo- in Pseudomonas aeruginosa (23), 2-hydroxyacid dehydrogenase lism and catabolism of D-2-HG are involved in L-serine biosynthesis (McyI) in Microcystis aeruginosa (24), and D-3-phosphoglycerate in Pseudomonas stutzeri A1501 and Pseudomonas aeruginosa PAO1.
    [Show full text]