Chapter 11 Lecture Notes: Carbohydrates
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Synechococcus Elongatus
bioRxiv preprint doi: https://doi.org/10.1101/2020.12.30.424818; this version posted December 31, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder.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. 1 5-Deoxyadenosine Salvage by Promiscuous Enzyme Activity 2 leads to Bioactive Deoxy-Sugar Synthesis in 3 Synechococcus elongatus 4 5 Running title: Unusual 5-deoxyadenosine salvage in S. elongatus 6 7 Johanna Rappa, Pascal Rathb, Joachim Kilianc, Klaus Brilisauera, Stephanie Grondb, Karl 8 Forchhammera# 9 aInterfaculty Institute of Microbiology and Infection Medicine, Microbiology/Organismic Interactions, Eberhard 10 Karls Universität Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany. 11 bInstitute of Organic Chemistry, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 18, 72076 Tübingen, 12 Germany. 13 cCenter for Plant Molecular Biology, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 32, 72076 14 Tübingen, Germany. 15 16 #corresponding author ([email protected], Tel.: +49 (7071) 29- 72096) 17 18 Abbreviations: SAM: S-Adenosylmethionine; MTA: Methylthioadenosine; 5dAdo: 19 5-Deoxyadenosine; MSP: Methionine salvage pathway; 5dR: 5-Deoxyribose; 7dSh: 20 7-Deoxysedoheptulose; 5dR-1P: 5-Deoxyribose 1-phosphate; 5dRu-1P: 5-Deoxyribulose 21 1-phosphate; MTRI: Methylthioribose 1-phosphate isomerase; MTR: Methylthioribose 22 23 Keywords: 5-Deoxyadenosine salvage, 5-deoxyribose, 7-deoxysedoheptulose, 7dSh 24 biosynthesis; enzyme promiscuity, S-adenosylmethionine, radical SAM enzymes, 25 cyanobacteria 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.12.30.424818; this version posted December 31, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. -
Monosaccharides and Their Derivatives in Carbonaceous Meteorites: a Scenario for Their Synthesis and Onset of Enantiomeric Excesses
life Review Monosaccharides and Their Derivatives in Carbonaceous Meteorites: A Scenario for Their Synthesis and Onset of Enantiomeric Excesses George Cooper 1,*, Andro C. Rios 1,2,* and Michel Nuevo 1,3 ID 1 NASA-Ames Research Center, Moffett Field, CA 94035, USA; [email protected] 2 Blue Marble Space, 1001 4th Ave, Ste 3201, Seattle, WA 98154, USA 3 Bay Area Environmental Research Institute, NASA Research Park, Moffett Field, CA 94035, USA * Correspondence: [email protected] (G.C.); [email protected] (A.C.R.) Received: 5 June 2018; Accepted: 22 August 2018; Published: 27 August 2018 Abstract: Carbonaceous meteorites provide the best glimpse into the solar system’s earliest physical and chemical processes. These ancient objects, ~4.56 billion years old, contain evidence of phenomena ranging from solar system formation to the synthesis of organic compounds by aqueous and (likely) low-temperature photolytic reactions. Collectively, chemical reactions resulted in an insoluble kerogen-like carbon phase and a complex mixture of discrete soluble compounds including amino acids, nucleobases, and monosaccharide (or “sugar”) derivatives. This review presents the documented search for sugars and their derivatives in carbonaceous meteorites. We examine early papers, published in the early 1960s, and note the analytical methods used for meteorite analysis as well as conclusions on the results. We then present the recent finding of sugar derivatives including sugar alcohols and several sugar acids: The latter compounds were found to possess unusual “D” enantiomeric (mirror-image) excesses. After discussions on the possible roles of interstellar grain chemistry and meteorite parent body aqueous activity in the synthesis of sugar derivatives, we present a scenario that suggests that most of Earth’s extraterrestrial sugar alcohols (e.g., glycerol) were synthesized by interstellar irradiation and/or cold grain chemistry and that the early solar disk was the location of the initial enantiomeric excesses in meteoritic sugar derivatives. -
Chapter 12 Slides
11/15/17 CHAPTER 12: Carbohydrates: Structure and Function OUTLINE • 12.1 Role of Carbohydrates • 12.2 Monosaccharides • 12.3 Complex Carbohydrates • 12.4 Carbohydrate Catabolism • 12.5 Oligosaccharides as Cell Markers CHAPTER 12: Carbohydrates: Structure and Function WHAT ARE CARBOHYDRATES? • Glucose and its derivatives are carbohydrates: Ø Carbohydrates are simple organic molecules that have a shared basic chemical Formula: Cn(H2O)n Ø The name “carbo + hydrate” represents that Fact that they are made from CO2 and H2O by photosynthesis • About halF oF all earth’s solid carbon is Found in two polymers of glucose found in plants: Ø Starch = major energy storage molecule Ø Cellulose = major structural component oF the plant cell wall (aka. “fiber”) CHAPTER 12: Carbohydrates: Structure and Function THE SIMPLEST CARBOHYDRATES • Monosaccharides are carbohydrates that cannot be hydrolyZed into simpler carbohydrates: Ø These are the Fundamental building blocks For all other carbohydrates (oFten called “simple sugars”) Ø All have Formulas of based on the basic pattern: Cn(H2O)n • Monosaccharides have speciFic Functional groups: 1. An aldehyde OR a ketone (not both!) 2. Several (two or more) alcohol (-OH) groups 1 11/15/17 CHAPTER 12: Carbohydrates: Structure and Function STRUCTURE & NOMENCLATURE OF MONOSACCHARIDES • Monosaccharides are classiFied by two features: 1. Length of their main carbon chain (utilize standard IUPAC naming For # oF carbons) 2. Whether they contain an aldehyde or ketone group • Names always end with –ose • Two common hexoses: -
A by Fluorous-Tag Assistance Th
Angewandte Chemie DOI: 10.1002/ange.200704262 Carbohydrate Microarrays Synthesis and Quantitative Evaluation of Glycero-d-manno-heptose Binding to Concanavalin A by Fluorous-Tag Assistance** Firoz A. Jaipuri, Beatrice Y. M. Collet, and Nicola L. Pohl* Herein we report the first use of a quantitative fluorous approach has proven valuable for the probing of other classes microarray strategy to show that the mannose-binding lectin of small molecules.[2] In the case of histone deacetylase concanavalin A (conA), contrary to prevailing belief, actually inhibitors with dissocation constants of less than 0.1s À1, the can accept modifications of the mannose at the C-6 position in hits found by fluorous microarrays were comparable to those the form of glycero-manno-heptoses found on pathogenic found by techniques such as surface plasmon resonance bacteria (Figure 1). The well-known mannose–conA interac- (SPR) and solution-based biochemical assays.[2a] Ideally, of course, the relative quantification of these binding interac- tions could also be carried out within the same fluorous microarray screening format. ConA is a plant lectin that is widely used like antibodies as research tools and diagnostics to identify the presence of specific sugars, such as mannose, on cells;[3] however, in reality the sugar specificities of lectins have not been tested broadly, especially against less readily available carbohydrates. ConA is the most-studied lectin and is usually considered to bind terminal alpha-linked mannose, glucose, and N-acetylglucos- amine. Earlier inhibition data suggest that modifications at the C-3, C-4, and C-6 positions of the d-mannopyranose deter binding to conA.[4] In particular, the loss of the hydroxy group in the C-6 position as in 6-deoxy-d-mannose and 1,6-anhydro- b-d-manno-pyranose result in complete loss of activity. -
(12) United States Patent (10) Patent No.: US 6,713,116 B1 Aldrich Et Al
USOO6713116B1 (12) United States Patent (10) Patent No.: US 6,713,116 B1 Aldrich et al. (45) Date of Patent: Mar. 30, 2004 (54) SWEET-STABLE ACIDIFIED BEVERAGES 4,957,763 A 9/1990 Saita et al. ................. 426/548 5,169,671. A 12/1992 Harada et al. .............. 426/658 (75) Inventors: Jessica A. Aldrich, Hazlet, NJ (US); 5,380,541 A 1/1995 Beyts et al. ................ 426/548 Lisa Y. Hanger, Basking Ridge, NJ 5.431,929 A 7/1995 Yatka et al. ................... 426/3 5,731,025 A 3/1998 Mitchell ..................... 426/548 (US); Guido Ritter, Laer (DE) 6,322,835 B1 * 11/2001 De Soete et al. ........... 426/453 (73) Assignee: Nutrinova Inc., Somerset, NJ (US) 6,372.277 B1 * 4/2002 Admiraal et al. ........... 426/548 FOREIGN PATENT DOCUMENTS (*) Notice: Subject to any disclaimer, the term of this patent is extended or adjusted under 35 W WO as: : 3.1. - - - - - - - - - - - A23L/1/236 U.S.C. 154(b) by 0 days. WO WO 98/19564 5/1998 ............. A23L/2/60 (21) Appl. No.: 09/675,825 OTHER PUBLICATIONS (22) Filed: Sep. 29, 2000 Widemann et al., “Synergistic Sweeteners”, Food Ingred. and Analysis Int., 19(6):51-52, 55-56 (abstract only), Dec. Related U.S. Application Data 1997.* (63) Continuation-in-part of application No. 09/186,275, filed on sk cited- by examiner Nov. 5, 1998, now abandoned. Primary Examiner Keith Hendricks (60) Pisional application No. 60/079,408, filed on Mar. 26, (74) Attorney, Agent, or Firm-ProPat, L.L.C. (51) Int. Cl. -
Carbohydrate Composition of Endotoxins from R-Type Isogenic Mutants of Shigella Sonnei Studied by Capillary Electrophoresis and GC-MS†
CROATICA CHEMICA ACTA CCACAA, ISSN 0011-1643, e-ISSN 1334-417X Croat. Chem. Acta 84 (3) (2011) 393–398. CCA-3487 Original Scientific Article Carbohydrate Composition of Endotoxins from R-type Isogenic Mutants of Shigella sonnei Studied by Capillary Electrophoresis and GC-MS† Annamária Bui,a Anikó Kilár,b,c Ágnes Dörnyei,a,c Viktória Poór,a Krisztina Kovács,b Béla Kocsis,b and Ferenc Kilára,c,* aInstitute of Bioanalysis, Faculty of Medicine, University of Pécs, Szigeti út 12., H-7624 Pécs bDepartment of Medical Microbiology and Immunology, Faculty of Medicine, University of Pécs, Szigeti út 12., H-7624 Pécs, Hungary cDepartment of Analytical and Environmental Chemistry, Faculty of Sciences, University of Pécs, Ifjúság útja 6., H-7624 Pécs, Hungary RECEIVED NOVEMBER 9, 2010; REVISED FEBRUARY 5, 2011; ACCEPTED MAY 13, 2011 Abstract. The carbohydrate composition of the rough-type endotoxins (lipopolysaccharides, LPSs) from Shigella sonnei mutant strains (Shigella sonnei phase II - 4303, 562H, R41 and 4350) was investigated by capillary electrophoresis and GC-MS. The monosaccharides obtained by hydrolysis were determined by capillary electrophoresis combined with laser induced fluorescence detection (CE-LIF) after labeling with 8-aminopyrene-1,3,6-trisulfonic acid (APTS) and by GC-MS as alditol-acetate derivatives. It was ob- tained that the lipopolysaccharides of the isogenic rough mutants are formed in a step-like manner, con- taining no heptose (4350), one D-glycero-D-mannoheptose (562H), or two or three L-glycero-D- mannoheptoses (R41, 4303, respectively) in the deep core region. Besides the heptoses, the longest LPS from the mutant Shigella sonnei 4303 contains hexoses, such as glucoses and galactoses, in a pro- portion of approximately 3:2. -
The Isolation and Partial Characterization of the Lipopolysaccharides from Rhizobium Leguminosarum Biovar Trifolii Strains TB4, TB104, and TB112 (Llne)
Eastern Illinois University The Keep Masters Theses Student Theses & Publications 1990 The solI ation and Partial Characterization of the Lipopolysaccharides from Rhizobium leguminosarum biovar trifolii strains TB4, TB104, and TB112 Jill K. Miller Eastern Illinois University This research is a product of the graduate program in Zoology at Eastern Illinois University. Find out more about the program. Recommended Citation Miller, Jill K., "The sI olation and Partial Characterization of the Lipopolysaccharides from Rhizobium leguminosarum biovar trifolii strains TB4, TB104, and TB112" (1990). Masters Theses. 2302. https://thekeep.eiu.edu/theses/2302 This is brought to you for free and open access by the Student Theses & Publications at The Keep. It has been accepted for inclusion in Masters Theses by an authorized administrator of The Keep. For more information, please contact [email protected]. THESIS REPRODUCTION CERTIFICATE TO: Graduate Degree Candidates who have written formal theses. SUBJECT: Permission to reproduce theses. The University Library is receiving a number of requests from other institutions asking permission to reproduce dissertations for inclusion in their library holdings. Although no copyright laws are involved, we feel that professional courtesy demands that permission be obtained from the author before we allow theses to be copied. Please sign one of the following statements: Booth Library of Eastern Illinois University has my permission to lend my thesis to a reputable college or university for the purpose of copying it for inclusion in that institution's library or research holdings. l f ttJ9o I Date I respectfully request Booth Library of Eastern Illinois University not allow my thesis be reproduced because -------------- Date Author m The Isolation and Partial Characterization of the Lipopolysaccharides from Rhizobium leguminosarum biovar trifolii strains TB4, TB104, and TB112 (llnE) BY Jill K. -
Deoxyketohexose Isomerase and Method for Producing Deoxyketohexose and Derivative Thereof Using the Same
(19) & (11) EP 2 161 332 A1 (12) EUROPEAN PATENT APPLICATION published in accordance with Art. 153(4) EPC (43) Date of publication: (51) Int Cl.: 10.03.2010 Bulletin 2010/10 C12N 9/90 (2006.01) C07H 3/02 (2006.01) C12P 19/24 (2006.01) C12N 15/09 (2006.01) (21) Application number: 07832172.6 (86) International application number: (22) Date of filing: 20.11.2007 PCT/JP2007/072442 (87) International publication number: WO 2008/062780 (29.05.2008 Gazette 2008/22) (84) Designated Contracting States: (72) Inventors: AT BE BG CH CY CZ DE DK EE ES FI FR GB GR • IZUMORI, Ken HU IE IS IT LI LT LU LV MC MT NL PL PT RO SE Kita-gun SI SK TR Kagawa 761-0793 (JP) • TOKUDA, Masaaki (30) Priority: 20.11.2006 JP 2006313671 Kita-gun Kagawa 761-0793 (JP) (71) Applicants: • FLEET, George • National University Corporation Kagawa OX27NB (GB) University • TSUJISAKA, Yoshio Takamatsu-shi, Kagawa 760-8521 (JP) Kita-gun • Rare Sugar Production Technical Kagawa 761-0615 (JP) Research Laboratories, LLC • TAKESHITA, Kei Mikicho Marugame-Shi Kita-gun Kagawa 763-8605 (JP) Kagawa 761-0615 (JP) • TSUSAKI, Keiji • Kabushiki Kaisha Hayashibara Seibutsu Okayama-Shi Kagaku Kenkyujo Okayama 712-8046 (JP) Okayama-shi • OKUMA, Kazuhiro Okayama 700-0907 (JP) Itami-shi • Matsutani Chemical Industry Co., Ltd. Hyogo 664-8508 (JP) Itami-shi, Hyogo 664-8508 (JP) (74) Representative: TBK-Patent Bavariaring 4-6 80336 München (DE) (54) DEOXYKETOHEXOSE ISOMERASE AND METHOD FOR PRODUCING DEOXYKETOHEXOSE AND DERIVATIVE THEREOF USING THE SAME (57) Providing 1- or 6-deoxy products corresponding to all of aldohexoses, ketohexoses and sugar alcohols, as based on Deoxy-Izumoring, as well as a method for systematically producing those products. -
Abstract Sugars and Related Polyols Are Critical Components of All
/ /) f t_/ 1 Abstract Sugars and related polyols are critical components of all organisms and may have been necessary for the origin of life. To date, this class of organic compounds had not been definitively identified in meteorites. This study was undertaken to determine if polyols were present in the early Solar System as constituents of carbonaceous meteorites. Results of analyses of the Murchison and Murray meteorites indicate that formaldehyde and sugar chemistry niay be responsible for the presence of a variety of polyols. We conclude that polyols were present on the early Earth through delivery by asteroids and possibly comets. .-) Sugar-Related Organic Compounds in Carbonaceous Meteorites George Cooper*, Novelle Kimmich, Warren Belisle, Josh Sarinana, Katrina Brabham, Laurence Garrel, G. Cooper, N. Kimmich, J. Sarinana, K. Brabham, W. Belisle, NASA Ames Research Center, Moffett Field, CA 94035 USA L. Garrel, current address, International Research Sch ool of Planetary Sciences (IRSPS), Universita' d'Annunzio Viale Pindaro, 42 65127 Pescara, Italy Carbonaceous meteorites contain a diverse suite of soluble organic compounds. To date, these compounds provide the only record available for the laboratory study of organic chemical processes in the early Solar System. The Murchison meteorite is the best-characterized carbonaceous meteorite with respect to organic chemistry. The study of its organic compounds has been important in understanding aqueous processes on carbonaceous meteorite parent bodies chemistry as well as the formation of compounds of potential importance for the origin of life. Among the classes of organic compounds found in Murchison are amino acids, amides, carboxylic acids, hydroxy acids, sulfonic acids, phosphonic acids, purines and pyrimidines (1). -
Inhibition of Fucosylation of Cell Wall Components by 2-Fluoro 2-Deoxy-L
The Plant Journal (2015) 84, 1137–1151 doi: 10.1111/tpj.13071 Inhibition of fucosylation of cell wall components by 2-fluoro 2-deoxy-L-fucose induces defects in root cell elongation Marie Dumont1, Arnaud Lehner1, Muriel Bardor1, Carole Burel1, Boris Vauzeilles2,3,4, Olivier Lerouxel5, Charles T. Anderson6, Jean-Claude Mollet1 and Patrice Lerouge1,* 1Laboratoire Glycobiologie et Matrice Extracellulaire Veg etale, EA 4358, IRIB, VASI, Normandie Universite, 76821 Mont-Saint-Aignan, France, 2Institut de Chimie Moleculaire et des Materiaux d’Orsay (ICMMO) UMR CNRS 8182, Universite de Paris Sud, 91405 Orsay, France, 3Institut de Chimie des Substances Naturelles (ICSN) UPR CNRS 2301, 91198 Gif-sur-Yvette, France, 4Click4Tag, Zone Luminy Biotech, Case 922, 163 Avenue de Luminy, 13009 Marseille, France, 5Centre de Recherches sur les Macromolecules Veg etales (CERMAV) – CNRS BP 53, 38041 Grenoble Cedex 9, France, and 6Department of Biology and Center for Lignocellulose Structure and Formation, Pennsylvania State University, University Park, Pennsylvania, USA Received 21 September 2015; revised 26 October 2015; accepted 3 November 2015; published online 13 November 2015. *For correspondence (e-mail [email protected]). SUMMARY Screening of commercially available fluoro monosaccharides as putative growth inhibitors in Arabidopsis thaliana revealed that 2-fluoro 2-L-fucose (2F-Fuc) reduces root growth at micromolar concentrations. The inability of 2F-Fuc to affect an Atfkgp mutant that is defective in the fucose salvage pathway indicates that 2F-Fuc must be converted to its cognate GDP nucleotide sugar in order to inhibit root growth. Chemical analysis of cell wall polysaccharides and glycoproteins demonstrated that fucosylation of xyloglucans and of N-linked glycans is fully inhibited by 10 lM 2F-Fuc in Arabidopsis seedling roots, but genetic evidence indicates that these alterations are not responsible for the inhibition of root development by 2F-Fuc. -
7 | Carbohydrates and Glycobiology
7 | Carbohydrates and Glycobiology Aldoses and Ketoses; Representative monosaccharides. (a)Two trioses, an aldose and a ketose. The carbonyl group in each is shaded. • An aldose contains an aldehyde functionality • A ketose contains a ketone functionality The Glycosidic Bond • Two sugar molecules can be joined via a glycosidic bond between an anomeric carbon and a hydroxyl carbon • The glycosidic bond (an acetal) between monomers is less reactive than the hemiacetal at the second monomer – Second monomer, with the hemiacetal, is reducing – Anomeric carbon involved in the glycosidic linkage is nonreducing • The disaccharide formed upon condensation of two glucose molecules via 1 4 bond is called maltose • Formation of maltose. A disaccharide is formed from two monosaccharides (here, two molecules of D-glucose) when an —OH (alcohol) of one glucose molecule (right) condenses with the intramolecular hemiacetal of the other glucose molecule (left), with elimination of H2O and formation of a glycosidic bond. The reversal of this reaction is hydrolysis—attack by H2O on the glycosidic bond. The maltose molecule, shown here as an illustration, retains a reducing hemiacetal at the C-1 not involved in the glycosidic bond. Because mutarotation interconverts the α and β forms of the hemiacetal, the bonds at this position are sometimes depicted with wavy lines, as shown here, to indicate that the structure may be either α or β. Nonreducing Disaccharides • Two sugar molecules can be also joined via a glycosidic bond between two anomeric carbons • The product has two acetal groups and no hemiacetals • There are no reducing ends, this is a nonreducing sugar • Trehalose is a constituent of hemolymph of insects • Two common disaccharides. -
Nucleotide Sugars in Chemistry and Biology
molecules Review Nucleotide Sugars in Chemistry and Biology Satu Mikkola Department of Chemistry, University of Turku, 20014 Turku, Finland; satu.mikkola@utu.fi Academic Editor: David R. W. Hodgson Received: 15 November 2020; Accepted: 4 December 2020; Published: 6 December 2020 Abstract: Nucleotide sugars have essential roles in every living creature. They are the building blocks of the biosynthesis of carbohydrates and their conjugates. They are involved in processes that are targets for drug development, and their analogs are potential inhibitors of these processes. Drug development requires efficient methods for the synthesis of oligosaccharides and nucleotide sugar building blocks as well as of modified structures as potential inhibitors. It requires also understanding the details of biological and chemical processes as well as the reactivity and reactions under different conditions. This article addresses all these issues by giving a broad overview on nucleotide sugars in biological and chemical reactions. As the background for the topic, glycosylation reactions in mammalian and bacterial cells are briefly discussed. In the following sections, structures and biosynthetic routes for nucleotide sugars, as well as the mechanisms of action of nucleotide sugar-utilizing enzymes, are discussed. Chemical topics include the reactivity and chemical synthesis methods. Finally, the enzymatic in vitro synthesis of nucleotide sugars and the utilization of enzyme cascades in the synthesis of nucleotide sugars and oligosaccharides are briefly discussed. Keywords: nucleotide sugar; glycosylation; glycoconjugate; mechanism; reactivity; synthesis; chemoenzymatic synthesis 1. Introduction Nucleotide sugars consist of a monosaccharide and a nucleoside mono- or diphosphate moiety. The term often refers specifically to structures where the nucleotide is attached to the anomeric carbon of the sugar component.