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INVESTIGATING THE COUPLING MECHANISM IN THE E. COLI MULTIDRUG TRANSPORTER, MdfA, BY FLUORESCENCE SPECTROSCOPY N. Fluman, D. Cohen-Karni, E. Bibi Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel In bacteria, multidrug transporters couple the energetically favored import of protons to export of chemically-dissimilar drugs (substrates) from the cell. By this function, they render bacteria resistant against multiple drugs. In this work, fluorescence spectroscopy of purified protein is used to unravel the mechanism of coupling between protons and substrates in MdfA, an E. coli multidrug transporter. Intrinsic fluorescence of MdfA revealed that binding of an MdfA substrate, tetraphenylphosphonium (TPP), induced a conformational change in this transporter. The measured affinity of MdfA-TPP was increased in basic pH, raising a possibility that TPP might bind tighter to the deprotonated state of MdfA. Similar increases in affinity of TPP also occurred (1) in the presence of the substrate chloramphenicol, or (2) when MdfA is covalently labeled by the fluorophore monobromobimane at a putative chloramphenicol interacting site. We favor a mechanism by which basic pH, chloramphenicol binding, or labeling with monobromobimane, all induce a conformational change in MdfA, which results in deprotonation of the transporter and increase in the affinity of TPP. PHENOTYPE CHARACTERIZATION OF AZOSPIRILLUM BRASILENSE Sp7 ABC TRANSPORTER (wzm) MUTANT A. Lerner1,2, S. Burdman1, Y. Okon1,2 1Department of Plant Pathology and Microbiology, Faculty of Agricultural, Food and Environmental Quality Sciences, Hebrew University of Jerusalem, Rehovot, Israel, 2The Otto Warburg Center for Agricultural Biotechnology, Faculty of Agricultural, Food and Environmental Quality Sciences, Hebrew University of Jerusalem, Rehovot, Israel Azospirillum, a free-living nitrogen fixer, belongs to the plant growth promoting rhizobacteria (PGPR), living in close association with plant roots. -
Rational Re-Design of Lactobacillus Reuteri 121 Inulosucrase for Product
RSC Advances View Article Online PAPER View Journal | View Issue Rational re-design of Lactobacillus reuteri 121 inulosucrase for product chain length control† Cite this: RSC Adv.,2019,9, 14957 Thanapon Charoenwongpaiboon,a Methus Klaewkla,ab Surasak Chunsrivirot,ab Karan Wangpaiboon,a Rath Pichyangkura,a Robert A. Field c and Manchumas Hengsakul Prousoontorn *a Fructooligosaccharides (FOSs) are well-known prebiotics that are widely used in the food, beverage and pharmaceutical industries. Inulosucrase (E.C. 2.4.1.9) can potentially be used to synthesise FOSs from sucrose. In this study, inulosucrase from Lactobacillus reuteri 121 was engineered by site-directed mutagenesis to change the FOS chain length. Three variants (R483F, R483Y and R483W) were designed, and their binding free energies with 1,1,1-kestopentaose (GF4) were calculated with the Rosetta software. R483F and R483Y were predicted to bind with GF4 better than the wild type, suggesting that these engineered enzymes should be able to effectively extend GF4 by one residue and produce a greater quantity of GF5 than the wild type. MALDI-TOF MS analysis showed that R483F, R483Y and R483W variants Creative Commons Attribution-NonCommercial 3.0 Unported Licence. could synthesise shorter chain FOSs with a degree of polymerization (DP) up to 11, 10, and 10, respectively, while wild type produced longer FOSs and in polymeric form. Although the decrease in catalytic activity and the increase of hydrolysis/transglycosylation activity ratio was observed, the variants could effectively Received 20th March 2019 synthesise FOSs with the yield up to 73% of substrate. Quantitative analysis demonstrated that these Accepted 7th May 2019 variants produced a larger quantity of GF5 than wild type, which was in good agreement with the predicted DOI: 10.1039/c9ra02137j binding free energy results. -
The Microbiota-Produced N-Formyl Peptide Fmlf Promotes Obesity-Induced Glucose
Page 1 of 230 Diabetes Title: The microbiota-produced N-formyl peptide fMLF promotes obesity-induced glucose intolerance Joshua Wollam1, Matthew Riopel1, Yong-Jiang Xu1,2, Andrew M. F. Johnson1, Jachelle M. Ofrecio1, Wei Ying1, Dalila El Ouarrat1, Luisa S. Chan3, Andrew W. Han3, Nadir A. Mahmood3, Caitlin N. Ryan3, Yun Sok Lee1, Jeramie D. Watrous1,2, Mahendra D. Chordia4, Dongfeng Pan4, Mohit Jain1,2, Jerrold M. Olefsky1 * Affiliations: 1 Division of Endocrinology & Metabolism, Department of Medicine, University of California, San Diego, La Jolla, California, USA. 2 Department of Pharmacology, University of California, San Diego, La Jolla, California, USA. 3 Second Genome, Inc., South San Francisco, California, USA. 4 Department of Radiology and Medical Imaging, University of Virginia, Charlottesville, VA, USA. * Correspondence to: 858-534-2230, [email protected] Word Count: 4749 Figures: 6 Supplemental Figures: 11 Supplemental Tables: 5 1 Diabetes Publish Ahead of Print, published online April 22, 2019 Diabetes Page 2 of 230 ABSTRACT The composition of the gastrointestinal (GI) microbiota and associated metabolites changes dramatically with diet and the development of obesity. Although many correlations have been described, specific mechanistic links between these changes and glucose homeostasis remain to be defined. Here we show that blood and intestinal levels of the microbiota-produced N-formyl peptide, formyl-methionyl-leucyl-phenylalanine (fMLF), are elevated in high fat diet (HFD)- induced obese mice. Genetic or pharmacological inhibition of the N-formyl peptide receptor Fpr1 leads to increased insulin levels and improved glucose tolerance, dependent upon glucagon- like peptide-1 (GLP-1). Obese Fpr1-knockout (Fpr1-KO) mice also display an altered microbiome, exemplifying the dynamic relationship between host metabolism and microbiota. -
Bacterial Exopolysaccharides: Biosynthesis Pathways and Engineering Strategies
REVIEW published: 26 May 2015 doi: 10.3389/fmicb.2015.00496 Bacterial exopolysaccharides: biosynthesis pathways and engineering strategies Jochen Schmid1*,VolkerSieber1 and Bernd Rehm2,3 1 Chair of Chemistry of Biogenic Resources, Technische Universität München, Straubing, Germany, 2 Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand, 3 The MacDiarmid Institute for Advanced Materials and Nanotechnology, Palmerston North, New Zealand Bacteria produce a wide range of exopolysaccharides which are synthesized via different biosynthesis pathways. The genes responsible for synthesis are often clustered within the genome of the respective production organism. A better understanding of the fundamental processes involved in exopolysaccharide biosynthesis and the regulation of these processes is critical toward genetic, metabolic and protein-engineering approaches to produce tailor-made polymers. These designer polymers will exhibit superior material properties targeting medical and industrial applications. Exploiting the Edited by: Weiwen Zhang, natural design space for production of a variety of biopolymer will open up a range of Tianjin University, China new applications. Here, we summarize the key aspects of microbial exopolysaccharide Reviewed by: biosynthesis and highlight the latest engineering approaches toward the production Jun-Jie Zhang, of tailor-made variants with the potential to be used as valuable renewable and Wuhan Institute of Virology, Chinese Academy of Sciences, China high-performance products -
Lactobacillus Rhamnosus HN001 1.1 Probiotic Bacteria
Copyright is owned by the Author of the thesis. Permission is given for a copy to be downloaded by an individual for the purpose of research and private study only. The thesis may not be reproduced elsewhere without the permission of the Author. DDiirreecctt sseelleeccttiioonn aanndd pphhaaggee ddiissppllaayy ooff tthhee LLaaccttoobbaacciilllluuss rrhhaammnnoossuuss HHNN000011 sseeccrreettoommee A thesis presented to Massey University in partial fulfillment of the requirements for the degree of Doctor of Philosophy by Dragana Jankovic 2008 Acknowledgments ii Acknowledgments I would like to thank the following people for the time, help, and support they have given me during my PhD work. Firstly and primarily I would like to thank my supervisor Dr Jasna Rakonjac for her encouragement, help, support, and expedience which were most appreciated. Her great scientific enthusiasm and amazing energy have been and will always be the inspiration for me. Also many thanks go to my cosupervisors Dr Mark Lubbers and Dr Michael Collett who were always a well of new ideas and discussion topics off all kinds. Their support was invaluable. I thank my cosupervisor Dr John Tweedie for helpful discussions and critical comments on my work. Special thanks to my office mates from Helipad lab, especially David Sheerin and Nicholas Bennett whose tolerance, patience and entertaining discussions were sometimes the only thing that kept me sane. Thanks to everyone at the Institute of Molecular BioSciences for their support. Thanks to them I looked forward to every coffee break to discuss new and interesting current issues. It was a pleasure and privilege working with such a great group of people. -
Structures and Characteristics of Carbohydrates in Diets Fed to Pigs: a Review Diego M
Navarro et al. Journal of Animal Science and Biotechnology (2019) 10:39 https://doi.org/10.1186/s40104-019-0345-6 REVIEW Open Access Structures and characteristics of carbohydrates in diets fed to pigs: a review Diego M. D. L. Navarro1, Jerubella J. Abelilla1 and Hans H. Stein1,2* Abstract The current paper reviews the content and variation of fiber fractions in feed ingredients commonly used in swine diets. Carbohydrates serve as the main source of energy in diets fed to pigs. Carbohydrates may be classified according to their degree of polymerization: monosaccharides, disaccharides, oligosaccharides, and polysaccharides. Digestible carbohydrates include sugars, digestible starch, and glycogen that may be digested by enzymes secreted in the gastrointestinal tract of the pig. Non-digestible carbohydrates, also known as fiber, may be fermented by microbial populations along the gastrointestinal tract to synthesize short-chain fatty acids that may be absorbed and metabolized by the pig. These non-digestible carbohydrates include two disaccharides, oligosaccharides, resistant starch, and non-starch polysaccharides. The concentration and structure of non-digestible carbohydrates in diets fed to pigs depend on the type of feed ingredients that are included in the mixed diet. Cellulose, arabinoxylans, and mixed linked β-(1,3) (1,4)-D-glucans are the main cell wall polysaccharides in cereal grains, but vary in proportion and structure depending on the grain and tissue within the grain. Cell walls of oilseeds, oilseed meals, and pulse crops contain cellulose, pectic polysaccharides, lignin, and xyloglucans. Pulse crops and legumes also contain significant quantities of galacto-oligosaccharides including raffinose, stachyose, and verbascose. -
Levan and Levansucrase-A Mini Review
INTERNATIONAL JOURNAL OF SCIENTIFIC & TECHNOLOGY RESEARCH VOLUME 4, ISSUE 05, MAY 2015 ISSN 2277-8616 Levan And Levansucrase-A Mini Review Bruna Caroline Marques Goncalves, Cristiani Baldo, Maria Antonia Pedrine Colabone Celligoi Abstract: Levansucrase is a fructosyltranferase that synthesizes levan and present great biotechnological interest. It’s being widely used in therapeutic, food, cosmetic and pharmaceutical industries. Levansucrase is produced by many microorganisms such as the Bacillus subtilis Natto using the sucrose fermentation. In this mini-review we described some properties and functions of this important group of enzymes and the recent technologies used in the production and purification of levansucrase and levan. Index Terms: Levan, levansucrase, fermentation, sucrose ———————————————————— 1 INTRODUCTION This enzyme contributes 60% of the extracellular sucrase The levansucrase (EC 2.4.1.10) is the best characterized activity, but it catalyses neither fructose polymerization into fructosyltranferases and are synthesize by most microbial levan nor degradation of polyfructose such as levan or inulin. levans by transferring a β(2→1)-D-frutosyl residue to the Thus, this enzyme differs from the B. subtilis SacC, which acceptor molecule (sucrose or levan) [1]. The database showed levanase activity in addition to sucrose hydrolysis. “carbohydrate-active enzymes” (CAZY) grouped the microbial FOUET et al. [5] characterized the precursor form of Bacillus levansucrases into glycoside hydrolases 68 family (GH68) due subtilis levansucrase and identified 3 structural genes induced to be able to act in specific substrate and share two catalytic, by sucrose. One of them, sacB, codify extracellular often acidic residues, acting as a protons donor and nucleophile levansucrase and 4 of 5 recognized regulatory loci are able to or general base, respectively [2]. -
Lehrstuhl Für Technische Mikrobiologie Sucrose Metabolism
Lehrstuhl für Technische Mikrobiologie Sucrose metabolism in lactobacilli and bifidobacteria Susanne B. Kaditzky Vollständiger Abdruck der von der Fakultät Wissenschaftszentrum Weihenstephan für Ernährung, Landnutzung und Umwelt der Technischen Universität München zur Erlangung des akademischen Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) genehmigten Dissertation. Vorsitzender: Univ.-Prof. Dr.-Ing., Dr.-Ing. habil. Werner Back Prüfer der Dissertation: 1. Univ.-Prof. Dr. rer. nat. habil. Rudi F. Vogel 2. Univ.-Prof. Dr. rer. nat. habil. Siegfried Scherer 3. Ass. Prof. Dr. rer. nat. Michael Gänzle, University of Alberta / Kanada (schriftliche Beurteilung) Die Dissertation wurde am 25.10.2007 bei der Technischen Universität München eingereicht und durch die Fakultät Wissenschaftszentrum Weihenstephan für Ernährung, Landnutzung und Umwelt am 07.01.2008 angenommen. Lehrstuhl für Technische Mikrobiologie Sucrose metabolism in lactobacilli and bifidobacteria Susanne B. Kaditzky Doctoral thesis Fakultät Wissenschaftszentrum Weihenstephan für Ernährung, Landnutzung und Umwelt Freising 2008 Mein Dank gilt Rudi Vogel für die Überlassung des Themas und seine geduldige und unterstützende Begleitung durch die lehrreichen und interessanten Jahre, Michael Gänzle, Maher Korakli und Daniel Meissner für ihr Engagement und ihre Unterstützung, allen Kollegen für das gute und humorvolle Arbeitsklima, Andreas Stocker für die Charakterisierung des EPS mit FFF, Peter Kaden für die NMR- Analyse und Jürgen Behr für die Durchführung der 2D-Experimente, -
Ep 1 117 822 B1
Europäisches Patentamt (19) European Patent Office & Office européen des brevets (11) EP 1 117 822 B1 (12) EUROPÄISCHE PATENTSCHRIFT (45) Veröffentlichungstag und Bekanntmachung des (51) Int Cl.: Hinweises auf die Patenterteilung: C12P 19/18 (2006.01) C12N 9/10 (2006.01) 03.05.2006 Patentblatt 2006/18 C12N 15/54 (2006.01) C08B 30/00 (2006.01) A61K 47/36 (2006.01) (21) Anmeldenummer: 99950660.3 (86) Internationale Anmeldenummer: (22) Anmeldetag: 07.10.1999 PCT/EP1999/007518 (87) Internationale Veröffentlichungsnummer: WO 2000/022155 (20.04.2000 Gazette 2000/16) (54) HERSTELLUNG VON POLYGLUCANEN DURCH AMYLOSUCRASE IN GEGENWART EINER TRANSFERASE PREPARATION OF POLYGLUCANS BY AMYLOSUCRASE IN THE PRESENCE OF A TRANSFERASE PREPARATION DES POLYGLUCANES PAR AMYLOSUCRASE EN PRESENCE D’UNE TRANSFERASE (84) Benannte Vertragsstaaten: (56) Entgegenhaltungen: AT BE CH CY DE DK ES FI FR GB GR IE IT LI LU WO-A-00/14249 WO-A-00/22140 MC NL PT SE WO-A-95/31553 (30) Priorität: 09.10.1998 DE 19846492 • OKADA, GENTARO ET AL: "New studies on amylosucrase, a bacterial.alpha.-D-glucosylase (43) Veröffentlichungstag der Anmeldung: that directly converts sucrose to a glycogen- 25.07.2001 Patentblatt 2001/30 like.alpha.-glucan" J. BIOL. CHEM. (1974), 249(1), 126-35, XP000867741 (73) Patentinhaber: Südzucker AG Mannheim/ • BUTTCHER, VOLKER ET AL: "Cloning and Ochsenfurt characterization of the gene for amylosucrase 68165 Mannheim (DE) from Neisseria polysaccharea: production of a linear.alpha.-1,4-glucan" J. BACTERIOL. (1997), (72) Erfinder: 179(10), 3324-3330, XP002129879 • GALLERT, Karl-Christian • DE MONTALK, G. POTOCKI ET AL: "Sequence D-61184 Karben (DE) analysis of the gene encoding amylosucrase • BENGS, Holger from Neisseria polysaccharea and D-60598 Frankfurt am Main (DE) characterization of the recombinant enzyme" J. -
Chemical and Functional Properties of Food Saccharides
Chemical and Functional Properties of Food Saccharides © 2004 by CRC Press LLC Chemical and Functional Properties of Food Components Series SERIES EDITOR Zdzislaw E. Sikorski Chemical and Functional Properties of Food Proteins Edited by Zdzislaw E. Sikorski Chemical and Functional Properties of Food Components, Second Edition Edited by Zdzislaw E. Sikorski Chemical and Functional Properties of Food Lipids Edited by Zdzislaw E. Sikorski and Anna Kolakowska Chemical and Functional Properties of Food Saccharides Edited by Piotr Tomasik © 2004 by CRC Press LLC Chemical and Functional Properties of Food Saccharides EDITED BY Piotr Tomasik CRC PRESS Boca Raton London New York Washington, D.C. © 2004 by CRC Press LLC 1486_C00.fm Page 4 Monday, September 8, 2003 8:01 AM Library of Congress Cataloging-in-Publication Data Chemical and functional properites of food saccharides / edited by Piotr Tomasik. p. cm. — (Chemical and functional properites of food components series ; 5) Includes bibliographical references and index. ISBN 0-8493-1486-0 (alk. paper) 1. Sweeteners. I. Tomasik, Piotr. II. Title. III. Series. TP421.C44 2003 664—dc21 2003053186 This book contains information obtained from authentic and highly regarded sources. Reprinted material is quoted with permission, and sources are indicated. A wide variety of references are listed. Reasonable efforts have been made to publish reliable data and information, but the author and the publisher cannot assume responsibility for the validity of all materials or for the consequences of their use. Neither this book nor any part may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, microfilming, and recording, or by any information storage or retrieval system, without prior permission in writing from the publisher. -
O O2 Enzymes Available from Sigma Enzymes Available from Sigma
COO 2.7.1.15 Ribokinase OXIDOREDUCTASES CONH2 COO 2.7.1.16 Ribulokinase 1.1.1.1 Alcohol dehydrogenase BLOOD GROUP + O O + O O 1.1.1.3 Homoserine dehydrogenase HYALURONIC ACID DERMATAN ALGINATES O-ANTIGENS STARCH GLYCOGEN CH COO N COO 2.7.1.17 Xylulokinase P GLYCOPROTEINS SUBSTANCES 2 OH N + COO 1.1.1.8 Glycerol-3-phosphate dehydrogenase Ribose -O - P - O - P - O- Adenosine(P) Ribose - O - P - O - P - O -Adenosine NICOTINATE 2.7.1.19 Phosphoribulokinase GANGLIOSIDES PEPTIDO- CH OH CH OH N 1 + COO 1.1.1.9 D-Xylulose reductase 2 2 NH .2.1 2.7.1.24 Dephospho-CoA kinase O CHITIN CHONDROITIN PECTIN INULIN CELLULOSE O O NH O O O O Ribose- P 2.4 N N RP 1.1.1.10 l-Xylulose reductase MUCINS GLYCAN 6.3.5.1 2.7.7.18 2.7.1.25 Adenylylsulfate kinase CH2OH HO Indoleacetate Indoxyl + 1.1.1.14 l-Iditol dehydrogenase L O O O Desamino-NAD Nicotinate- Quinolinate- A 2.7.1.28 Triokinase O O 1.1.1.132 HO (Auxin) NAD(P) 6.3.1.5 2.4.2.19 1.1.1.19 Glucuronate reductase CHOH - 2.4.1.68 CH3 OH OH OH nucleotide 2.7.1.30 Glycerol kinase Y - COO nucleotide 2.7.1.31 Glycerate kinase 1.1.1.21 Aldehyde reductase AcNH CHOH COO 6.3.2.7-10 2.4.1.69 O 1.2.3.7 2.4.2.19 R OPPT OH OH + 1.1.1.22 UDPglucose dehydrogenase 2.4.99.7 HO O OPPU HO 2.7.1.32 Choline kinase S CH2OH 6.3.2.13 OH OPPU CH HO CH2CH(NH3)COO HO CH CH NH HO CH2CH2NHCOCH3 CH O CH CH NHCOCH COO 1.1.1.23 Histidinol dehydrogenase OPC 2.4.1.17 3 2.4.1.29 CH CHO 2 2 2 3 2 2 3 O 2.7.1.33 Pantothenate kinase CH3CH NHAC OH OH OH LACTOSE 2 COO 1.1.1.25 Shikimate dehydrogenase A HO HO OPPG CH OH 2.7.1.34 Pantetheine kinase UDP- TDP-Rhamnose 2 NH NH NH NH N M 2.7.1.36 Mevalonate kinase 1.1.1.27 Lactate dehydrogenase HO COO- GDP- 2.4.1.21 O NH NH 4.1.1.28 2.3.1.5 2.1.1.4 1.1.1.29 Glycerate dehydrogenase C UDP-N-Ac-Muramate Iduronate OH 2.4.1.1 2.4.1.11 HO 5-Hydroxy- 5-Hydroxytryptamine N-Acetyl-serotonin N-Acetyl-5-O-methyl-serotonin Quinolinate 2.7.1.39 Homoserine kinase Mannuronate CH3 etc. -
University of Groningen Glycosidic Bond Specificity of Glucansucrases
University of Groningen Glycosidic bond specificity of glucansucrases Leemhuis, Hans; Pijning, Tjaard; Dobruchowska, Justyna M.; Dijkstra, Bauke W.; Dijkhuizen, Lubbert Published in: Biocatalysis and Biotransformation DOI: 10.3109/10242422.2012.676301 IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from it. Please check the document version below. Document Version Publisher's PDF, also known as Version of record Publication date: 2012 Link to publication in University of Groningen/UMCG research database Citation for published version (APA): Leemhuis, H., Pijning, T., Dobruchowska, J. M., Dijkstra, B. W., & Dijkhuizen, L. (2012). Glycosidic bond specificity of glucansucrases: on the role of acceptor substrate binding residues. Biocatalysis and Biotransformation, 30(3), 366-376. DOI: 10.3109/10242422.2012.676301 Copyright Other than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons). Take-down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons the number of authors shown on this cover page is limited to 10 maximum. Download date: 11-02-2018 Biocatalysis and Biotransformation, May–June 2012; 30(3): 366–376 ORIGINAL ARTICLE Glycosidic bond specifi city of glucansucrases: on the role of acceptor substrate binding residues HANS LEEMHUIS 1 , TJAARD PIJNING 2 , JUSTYNA M.