DOCSLIB.ORG

Microbial Biochemistry, 2Nd Edition

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Microbial Biochemistry, 2Nd Edition Microbial Biochemistry . G.N. Cohen Microbial Biochemistry Second Edition Prof. G.N. Cohen Institut Pasteur rue du Docteur Roux 28 75724 Paris France [email protected] ISBN 978-90-481-9436-0 e-ISBN 978-90-481-9437-7 DOI 10.1007/978-90-481-9437-7 Springer Dordrecht Heidelberg London New York Library of Congress Control Number: 2010938472 # Springer Science+Business Media B.V. 2011 No part of this work may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, microfilming, recording or otherwise, without written permission from the Publisher, with the exception of any material supplied specifically for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work. Printed on acid-free paper Springer is part of Springer Science+Business Media (www.springer.com) Foreword This book originates from almost 60 years of living in the company of micro- organisms, mainly with Escherichia coli. My scientific life has taken place almost exclusively at the Institut Pasteur in Paris, where many concepts of modern molecular biology were born or developed. The present work emphasizes the interest of microbial physiology, biochemistry and genetics. It takes into account the considerable advances which have been made in the field in the last 30 years by the introduction of gene cloning and sequencing and by the exponential development of physical methods such as X-ray crystallog- raphy of proteins. The younger generation of biochemists is legitimately interested in the problems raised by differentiation and development in higher organisms, and also in neuros- ciences. It is however my feeling that the study of prokaryotes will remain for a long time the best introduction to general biology. A particular emphasis has been given to particular systems which have been extensively studied from historical, physiological, enzymological, structural, genetic and evolutionary points of view: I present my apologies to those who may find that this choice is too personal and reflects too much my personal interest in subjects in which I have either a personal contribution or where important results have been obtained by some of my best friends. I am grateful to the Philippe Foundation for the help it has given to me and to many of my students for many years. My thanks are due to my wife, Louisette Cohen for her patience and help, not only while this book was written, but also during our near 70 years common life. This work is a tribute to the memory of my beloved colleagues, my mentor Jacques Monod, and the late Harold Amos, Dean B. Cowie, Michael Doudoroff, Ben Nisman, Earl R. Stadtman, Roger Y. Stanier, Germaine Stanier, Huguette and Kissel Szulmajster. Paris, France G.N. Cohen v . Contents 1 Bacterial Growth ..............................................................1 The Lag Phase ..................................................................1 The Exponential Phase..........................................................1 Linear Growth...................................................................2 The Yield of Growth............................................................3 Variation of the Growth Rate at Limiting Carbon Source Concentrations ..................................................................4 Continuous Growth: The Chemostat ...........................................5 Advantages of the Continuous Exponential Culture ...........................7 Diauxic Growth .................................................................7 Selected References........................................................... 10 2 The Outer Membrane of Gram-negative Bacteria and the Cytoplasmic Membrane ........................................... 11 The Outer Membrane of Gram-Negative Bacteria .. ......................... 11 The Cytoplasmic Membrane.................................................. 12 Energy Generation ............................................................ 13 ATP Synthase .............................................................. 13 Subunit Composition of the ATP Synthase .................................. 14 ATP Synthesis in Archaea .................................................... 16 Selected References........................................................... 16 3 Peptidoglycan Synthesis and Cell Division ................................ 17 General Structure ............................................................. 17 Assembly of the Peptidoglycan Unit ......................................... 18 The Membrane Steps ......................................................... 19 Assembly of the Murein Sacculus ............................................ 20 Penicillin Sensitivity .......................................................... 20 Cell Division . ................................................................. 21 Selected References........................................................... 22 vii viii Contents 4 Cellular Permeability ....................................................... 23 Accumulation, Crypticity, and Selective Permeability....................... 24 b-Galactoside Permease....................................................... 25 Accumulation in Induced Cells: Kinetics and Specificity ................. 26 The Induced Synthesis of Galactoside Permease . ......................... 29 Functional Significance of Galactoside Permease: Specific Crypticity ... 30 Functional Relationships of Permease: Induction ......................... 32 Genetic Relationships of Galactosidase and Galactoside Permease... ................................................................. 32 Galactoside Permease as Protein........................................... 33 Periplasmic Binding Proteins and ATP Binding Cassettes................... 36 Phosphotransferases: The PTS System ....................................... 39 TRAP Transporters ........................................................... 41 A Few Well-identified Cases of Specific Cellular Permeability ............. 42 Amino Acid Permeases .................................................... 42 Peptide Permeases.......................................................... 43 Porins.......................................................................... 45 Iron Uptake... ................................................................. 47 Conclusion ... ................................................................. 48 Selected References........................................................... 48 5 Allosteric Enzymes .......................................................... 51 Allosteric Inhibition and Activation .......................................... 54 An Alternative Model......................................................... 61 Conclusion ... ................................................................. 62 Selected References........................................................... 62 6 Glycolysis, Gluconeogenesis and Glycogen Synthesis .................... 63 Glycogen Degradation ........................................................ 63 Glycolysis ..................................................................... 63 Hexokinase ................................................................. 65 Glucose 6-Phosphate Isomerase............................................ 65 Phosphofructokinase ....................................................... 66 Fructose 1,6-Bisphosphate Aldolase ....................................... 68 Triose Phosphate Isomerase................................................ 68 Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH).................. 68 Phosphoglycerate Kinase................................................... 69 Phosphoglyceromutase ..................................................... 69 Enolase ..................................................................... 69 Pyruvate Kinase ............................................................ 70 Gluconeogenesis .............................................................. 70 Fructose Bisphosphatase in Microorganisms ................................. 70 Glycogen Synthesis ........................................................... 71 Glycogen Synthase ......................................................... 71 Contents ix Control of Glycogen Biosynthesis ............................................ 72 Branching Enzyme ............................................................ 72 7 The Pentose Phosphate and Entner–Doudoroff Pathways ............... 73 The Pentose Phosphate Pathway.............................................. 73 The Enzymes of the Oxidative Phase......................................... 73 Glucose 6-Phosphate Dehydrogenase...................................... 73 6-Phosphogluconolactonase ................................................ 74 6-Phosphogluconate Dehydrogenase (Decarboxylating) .................. 74 Ribose Phosphate Isomerase ............................................... 74 The Enzymes of the Non-oxidative Phase.................................... 74 Transketolase ............................................................... 75 Transaldolase ............................................................... 76 Ribulose-5-Phosphate-3-Epimerase........................................ 76 Regulation of the Pentose Phosphate Pathway ............................... 77 The Entner–Doudoroff Pathway ........................................... 77 8 The Tricarboxylic Acid Cycle and the Glyoxylate Bypass
Load more

Recommended publications
  • (10) Patent No.: US 8119385 B2
    US008119385B2 (12) United States Patent (10) Patent No.: US 8,119,385 B2 Mathur et al. (45) Date of Patent: Feb. 21, 2012 (54) NUCLEICACIDS AND PROTEINS AND (52) U.S. Cl. ........................................ 435/212:530/350 METHODS FOR MAKING AND USING THEMI (58) Field of Classification Search ........................ None (75) Inventors: Eric J. Mathur, San Diego, CA (US); See application file for complete search history. Cathy Chang, San Diego, CA (US) (56) References Cited (73) Assignee: BP Corporation North America Inc., Houston, TX (US) OTHER PUBLICATIONS c Mount, Bioinformatics, Cold Spring Harbor Press, Cold Spring Har (*) Notice: Subject to any disclaimer, the term of this bor New York, 2001, pp. 382-393.* patent is extended or adjusted under 35 Spencer et al., “Whole-Genome Sequence Variation among Multiple U.S.C. 154(b) by 689 days. Isolates of Pseudomonas aeruginosa” J. Bacteriol. (2003) 185: 1316 1325. (21) Appl. No.: 11/817,403 Database Sequence GenBank Accession No. BZ569932 Dec. 17. 1-1. 2002. (22) PCT Fled: Mar. 3, 2006 Omiecinski et al., “Epoxide Hydrolase-Polymorphism and role in (86). PCT No.: PCT/US2OO6/OOT642 toxicology” Toxicol. Lett. (2000) 1.12: 365-370. S371 (c)(1), * cited by examiner (2), (4) Date: May 7, 2008 Primary Examiner — James Martinell (87) PCT Pub. No.: WO2006/096527 (74) Attorney, Agent, or Firm — Kalim S. Fuzail PCT Pub. Date: Sep. 14, 2006 (57) ABSTRACT (65) Prior Publication Data The invention provides polypeptides, including enzymes, structural proteins and binding proteins, polynucleotides US 201O/OO11456A1 Jan. 14, 2010 encoding these polypeptides, and methods of making and using these polynucleotides and polypeptides.
    [Show full text]
  • SI Appendix Index 1
    SI Appendix Index Calculating chemical attributes using EC-BLAST ................................................................................ 2 Chemical attributes in isomerase reactions ............................................................................................ 3 Bond changes …..................................................................................................................................... 3 Reaction centres …................................................................................................................................. 5 Substrates and products …..................................................................................................................... 6 Comparative analysis …........................................................................................................................ 7 Racemases and epimerases (EC 5.1) ….................................................................................................. 7 Intramolecular oxidoreductases (EC 5.3) …........................................................................................... 8 Intramolecular transferases (EC 5.4) ….................................................................................................. 9 Supporting references …....................................................................................................................... 10 Fig. S1. Overview …............................................................................................................................
    [Show full text]
  • 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.
    [Show full text]
  • Computational Genome and Pathway Analysis of Halophilic Archaea
    Computational Genome and Pathway Analysis of Halophilic Archaea Dissertation Michaela Falb aus Heiligenstadt (Eichsfeld) 2005 Dissertation zur Erlangung des Doktorgrades der Fakultät für Chemie und Pharmazie der Ludwig-Maximilians-Universität München Computational Genome and Pathway Analysis of Halophilic Archaea Michaela Falb aus Heiligenstadt (Eichsfeld) 2005 Erklärung Diese Dissertation wurde im Sinne von §13 Abs. 3 bzw. 4 der Promotionsordnung vom 29. Januar 1998 von Prof. Dr. Dieter Oesterhelt betreut. Ehrenwörtliche Versicherung Diese Dissertation wurde selbständig, ohne unerlaubte Hilfe erarbeitet. München, den 31. August 2005 Michaela Falb Dissertation eingereicht am: 01.09.2005 1. Gutachter: Prof. Dr. Dieter Oesterhelt 2. Gutachter: Prof. Dr. Erich Bornberg-Bauer Mündliche Prüfung am: 22.12.2005 CONTENTS Summary 1 1 Introduction to Halophilic Archaea 3 1.1 Hypersaline environments 3 1.2 Taxononomy of halophilic archaea 5 1.3 Information processing in archaea 7 1.4 Physiology and metabolism of halophilic archaea 9 1.4.1 Osmotic adaptation 9 1.4.2 Nutritional demands, nutrient transport and sensing 10 1.4.3 Energy metabolism 11 1.5 Genomes of halophilic archaea 13 1.6 Motivation 15 2 Gene Prediction and Start Codon Selection in Halophilic Genomes 17 2.1 Introduction 17 2.2 Post-processing of gene prediction results by expert validation 19 2.3 Intrinsic features of haloarchaeal proteins and gene context analysis 22 2.3.1 Isoelectric points and amino acid distribution of halophilic proteins 22 2.3.2 Development of a pI scanning tool
    [Show full text]
  • Natural Occurrence and Industrial Applications of D-Amino Acids: an Overview
    CHEMISTRY & BIODIVERSITY – Vol. 7 (2010) 1531 REVIEW Natural Occurrence and Industrial Applications of d-Amino Acids: An Overview by Sergio Martnez-Rodrguez*, Ana Isabel Martnez-Go´ mez, Felipe Rodrguez-Vico, Josefa Mara Clemente-Jime´nez, Francisco Javier Las Heras-Va´zquez* Dpto. Qumica Fsica, Bioqumica y Qumica Inorga´nica, Universidad de Almera, Edificio CITE I, Carretera de Sacramento s/n, 04120 La Can˜ ada de San Urbano, Almera, Spain (S. M.-R.: phone: þ34950015850; fax: þ34950015615; F. J. H.-V.: phone: þ34950015055; fax: þ34950015615) Interest in d-amino acids has increased in recent decades with the development of new analytical methods highlighting their presence in all kingdoms of life. Their involvement in physiological functions, and the presence of metabolic routes for their synthesis and degradation have been shown. Furthermore, d-amino acids are gaining considerable importance in the pharmaceutical industry. The immense amount of information scattered throughout the literature makes it difficult to achieve a general overview of their applications. This review summarizes the state-of-the-art on d-amino acid applications and occurrence, providing both established and neophyte researchers with a comprehensive introduction to this topic. Introduction. – Since Miller established in 1953 that amino acids were most probably present in the primitive Earths atmosphere [1], one of the largest mysteries in science has been why evolution chose the l-isomer of a-amino acids for the emergence of life. While, from the chemical-physical point of view, enantiomeric enhancement in the prebiotic scenario of l-amino acids is plausible [2][3], the most broadly accepted theory is that primitive life acquired polymers by an as yet unknown mechanism.
    [Show full text]
  • 12) United States Patent (10
    US007635572B2 (12) UnitedO States Patent (10) Patent No.: US 7,635,572 B2 Zhou et al. (45) Date of Patent: Dec. 22, 2009 (54) METHODS FOR CONDUCTING ASSAYS FOR 5,506,121 A 4/1996 Skerra et al. ENZYME ACTIVITY ON PROTEIN 5,510,270 A 4/1996 Fodor et al. MICROARRAYS 5,512,492 A 4/1996 Herron et al. 5,516,635 A 5/1996 Ekins et al. (75) Inventors: Fang X. Zhou, New Haven, CT (US); 5,532,128 A 7/1996 Eggers Barry Schweitzer, Cheshire, CT (US) 5,538,897 A 7/1996 Yates, III et al. s s 5,541,070 A 7/1996 Kauvar (73) Assignee: Life Technologies Corporation, .. S.E. al Carlsbad, CA (US) 5,585,069 A 12/1996 Zanzucchi et al. 5,585,639 A 12/1996 Dorsel et al. (*) Notice: Subject to any disclaimer, the term of this 5,593,838 A 1/1997 Zanzucchi et al. patent is extended or adjusted under 35 5,605,662 A 2f1997 Heller et al. U.S.C. 154(b) by 0 days. 5,620,850 A 4/1997 Bamdad et al. 5,624,711 A 4/1997 Sundberg et al. (21) Appl. No.: 10/865,431 5,627,369 A 5/1997 Vestal et al. 5,629,213 A 5/1997 Kornguth et al. (22) Filed: Jun. 9, 2004 (Continued) (65) Prior Publication Data FOREIGN PATENT DOCUMENTS US 2005/O118665 A1 Jun. 2, 2005 EP 596421 10, 1993 EP 0619321 12/1994 (51) Int. Cl. EP O664452 7, 1995 CI2O 1/50 (2006.01) EP O818467 1, 1998 (52) U.S.
    [Show full text]
  • Supplementary Figure 1. Rpod Sequence Alignment. Protein Sequence Alignment Was Performed for Rpod from Three Species, Pseudoruegeria Sp
    J. Microbiol. Biotechnol. https://doi.org/10.4014/jmb.1911.11006 J. Microbiol. Biotechnol. https://doi.org/10.4014/jmb.2003.03025 Supplementary Figure 1. RpoD sequence alignment. Protein sequence alignment was performed for RpoD from three species, Pseudoruegeria sp. M32A2M (FPS10_24745, this study), Ruegeria pomeroyi (NCBI RefSeq: WP_011047484.1), and Escherichia coli (NCBI RefSeq: NP_417539.1). Multalin version 5.4.1 was used for the analysis. Subregion 2 and 4 are represented in a rectangle, and the helix-turn-helix motif in subregion 4 is highlighted in red. The amino acid degeneration from any of the three was highlighted in light gray and the sequence degeneration between Pseudoruegeria sp. M32A2M and R. pomeroyi is highlighted in dark gray. The substituted two amino acids into HTH motif (K578Q and D581S) against E. coli were marked as asterisk. Supplementary Table 1. Genome assembly statistics Categories Pseudoruegeria sp. M32A2M Number of scaffolds less than 1,000 bp 0 Number of scaffolds between 1,000 bp –10,000 bp 39 Number of scaffolds between 10,000 bp – 100,000 bp 38 Number of scaffolds larger than 100,000 bp 14 Number of scaffolds 91 Total assembled length (bp) 5,466,515 G+C contents (%) 62.4 N50 (bp) 249,384 Minimum length of scaffold (bp) 1,015 Maximum length of scaffold (bp) 733,566 Total Ns included in the draft genome 2,158 Supplementary Table 2. The list of gene annotation and its functional categorization in Pseudoruegeria sp.
    [Show full text]
  • Lawrence Berkeley National Laboratory Recent Work
    Lawrence Berkeley National Laboratory Recent Work Title PROTONATED AMINO ACID PRECURSOR STUDIES OH RHODOTORULIC ACID BIOSYNTHESIS IN DEUTERIUM OXIDE MEDIA Permalink https://escholarship.org/uc/item/0w01t99f Author Akers, Hugh A. Publication Date 1972-06-01 eScholarship.org Powered by the California Digital Library University of California ., ~ " .... ,) Submitted to Biochemistry LBL-957 Preprint:· - PROTONATED AMINO ACID PRECURSOR STUDIES ON RHODOTORU LIC ACID BIOSYNTHESIS IN DEUTERIUM OXIDE MEDIA Hugh A. Akers, Miguel Llincrs and J. B. Neilands June 1972 AEC Contract No. W-7405-eng-48 -For Reference Not to be taken from this room DISCLAIMER This document was prepared as an account of work sponsored by the United States Government. While this document is believed to contain correct information, neither the United States Government nor any agency thereof, nor the Regents of the University of California, nor any of their employees, makes any warranty, express or implied, or assumes any legal responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights. Reference herein to any specific commercial product, process, or service by its trade name, trademark, manufacturer, or otherwise, does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof, or the Regents of the University of California. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof or the Regents of the University of California. -\ ·.1 ~ -~ ,,} U ~, ( . J Protonatcd Amino Acid Precursor Studies on Rhodotorulic Acid Biosynthesis in Deuterium Oxide Media* t ~ t I~gh A.
    [Show full text]
  • ATP-Getriebener Elektronentransfer Bei Der Enzymatischen Dehydratisierung Von (R)-2- Hydroxyglutaryl-Coa Zu (E)-Glutaconyl-Coa in Clostridien
    ATP-getriebener Elektronentransfer bei der enzymatischen Dehydratisierung von (R)-2- Hydroxyglutaryl-CoA zu (E)-Glutaconyl-CoA in Clostridien Dissertation zur Erlangung des Doktorgrades der Naturwissenschaften (Dr. rer. nat.) dem Fachbereich Biologie der Philipps-Universität Marburg vorgelegt von Marcus Hans aus Koblenz Marburg/Lahn 2000 ii Vom Fachbereich Biologie der Philipps-Universität Marburg als Dissertation am __________________ angenommen Erstgutachter: Prof. Dr. W. Buckel Zweitgutachter: Prof. Dr. R.K. Thauer Tag der mündlichen Prüfung am ____________________________________ iii Inhaltsverzeichnis Seite Deckblatt i Fachbereichserklärung ii Inhaltsverzeichnis iii-vii Abkürzungsverzeichnis 1 Zusammenfassung 2-3 Einleitung 4-26 1. Anaerober Glutamatabbau 4 2. Eisen-Schwefel-Cluster und Flavine in Proteinen 8 2.1 EPR- und Mössbauer-Spektroskopie an Eisen-Schwefel-Proteinen 13 2.1.1 Grundlagen der EPR-Spektroskopie 13 2.1.2 Grundlagen der Mössbauer-Spektroskopie 16 3. (R)-2-Hydroxyglutaryl-CoA-Dehydratase 18 4. Zum Mechanismus der (R)-2-Hydroxyglutaryl-CoA-Dehydratase 21 5. Zielsetzung der Arbeit 26 Material und Methoden 27-53 1. Verwendetes Material 27 1.1 Chemikalien und Biochemikalien 27 1.2 Gase 27 1.3 Säulenmaterialien und Geräte 27 1.4 Bakterien 29 1.4.1 Acidaminococcus fermentans 29 1.4.2 Clostridium symbiosum HB25 30 1.4.3 Escherichia coli XL1-blue MRF‘ 31 1.4.4 Escherichia coli BL21 (DE3) 31 1.5 Plasmide 31 2. Molekularbiologische Methoden 32 2.1 Verwendete Puffer 32 2.2 Agarose-Gelelektrophorese von DNA-Fragmenten 32 2.3 Restriktion von DNA 32 2.4 Reinigung der DNA-Fragmente 33 2.5 Ligation von DNA 33 iv 2.6 Plasmid-Minipräparation 33 2.6.1 Midipräparation von Plasmid-DNA 34 2.6.2 Photometrische Konzentrationsbestimmung doppelsträngiger DNA 34 2.7 Präparation kompetenter E.
    [Show full text]
  • Bacterial Citrate Lyase
    J. Biosci., Vol. 6, Number 4, October 1984, pp. 379–401. © Printed in India. Bacterial citrate lyase SUBHALAKSHMI SUBRAMANIAN and C. SIVARAMAN* Biochemistry Division, National Chemical Laboratory, Poona 411 008, India MS received 30 July 1984 Abstract. Bacterial citrate lyase, the key enzyme in fermentation of citrate, has interesting structural features. The enzyme is a complex assembled from three non-identical subunits, two having distinct enzymatic activities and one functioning as an acyl-carrier protein. Bacterial citrate lyase, si-citrate synthase and ATP-citrate lyase have similar stereospecificities and show cofactor cross-reactions. On account of these common features, the citrate enzymes are promising markers in the study of evolutionary biology. The occurrence, function, regulation and structure of bacterial citrate lyase are reviewed in this article. Keywords. Bacterial citrate lyase; anaerobic citrate utilization; citrate lyase autoinactivation; subunit structure and function; subunit stoichiometry; active sites; citrate lyase prosthetic group. Citrate enzymes Citrate occupies a central position in intermediary metabolism and the enzymes involved in its formation or breakdown have special importance. Four different groups of enzymes are known which catalyze the synthesis (or dissimilation) of citrate through an aldol- (or retroaldol-) type reaction involving an equilibrium between citrate on the one hand and oxaloacetate and an acetyl-moiety on the other. These are: – (i) Bacterial citrate lyase [citrate oxaloacetate-lyase (pro-3S-CH 2COO → acetate); EC 4.1.3.6] found as yet only in procaryotes, which catalyzes the cleavage of citrate into oxaloacetate and acetate in the presence of divalent metal ions such as Mg2 + or Mn2 +. Citrate oxaloacetate + acetate (ii) ATP-citrate lyase [ATP: .
    [Show full text]
  • Metabolic Responses to Potassium Availability and Waterlogging in Two Oil- Producing Species: Sunflower and Oil Palm
    Metabolic responses to potassium availability and waterlogging in two oil- producing species: sunflower and oil palm Jing Cui Supervisor: Prof. Guillaume Tcherkez A thesis submitted for the degree of Doctor of Philosophy The Australian National University Declaration Except where otherwise indicated, this thesis is my own original work. No portion of the work presented in this thesis has been submitted for another degree. Jing Cui Research School of Biology College of Medicine, Biology and Environment September, 2019 © Copyright by Jing Cui (2019). All Rights Reserved. 1 Acknowledgements Primarily my deepest thank goes to my principal supervisor Professor Guillaume Tcherkez (Research School of Biology, The Australian National University, Canberra), who has always given me help, advice and support throughout my PhD, Thank you very much for your enthusiasm, patience, efficience and guidance. One of the major motivations I committed to this PhD is your strong faith in me, I have been truly fortunate to work with you for the last three years. I thank my co-supervisor Dr. Emmanuelle Lamade (CIRAD, France), for your time, thoughtful comments and invaluable advice that they gave me along my project. Thank you also to my PhD committee members Dr. Adam Carroll (Research School of Chemistry and Biology Joint Mass Spectrometry Facility), Dr. Cyril Abadie, Dr. Hilary Stuart-Williams and Prof. Marilyn Ball (Research School of Biology, The Australian National University) for their help and guidance. I would like to thank Dr Thy Truong (Research School of Chemistry and Biology Joint Mass Spectrometry Facility) for taking the time to share with me her expertise in GC-MS, and look forward to working with her in LC/MSMS, also thank Dr.Marlène Davanture and Dr.
    [Show full text]
  • Hyper Ammonia Producing Bacteria and Bacteriophages in the Rumen Microbiome
    STUDYING THE UNDERSTUDIED: HYPER AMMONIA PRODUCING BACTERIA AND BACTERIOPHAGES IN THE RUMEN MICROBIOME by Jessica Charlotte Abigail Friedersdorff A thesis submitted in partial fulfillment of the requirements for the degree of PhD in Biological Sciences Aberystwyth University 2020 Preface I. Mandatory Layout of Declaration/Statements Word Count of thesis: 62,288 DECLARATION This work has not previously been accepted in substance for any degree and is not being concurrently submitted in candidature for any degree. Candidate name Jessica Charlotte Abigail Friedersdorff Signature: Date 15/09/2020 STATEMENT 1 This thesis is the result of my own investigations, except where otherwise stated. Where *correction services have been used, the extent and nature of the correction is clearly marked in a footnote(s). Other sources are acknowledged by footnotes giving explicit references. A bibliography is appended. Signature: Date 15/09/2020 [*this refers to the extent to which the text has been corrected by others] STATEMENT 2 I hereby give consent for my thesis, if accepted, to be available for photocopying and for inter-library loan, and for the title and summary to be made available to outside organisations. Signature: Date 15/09/2020 NB: Candidates on whose behalf a bar on access (hard copy) has been approved by the University should use the following version of Statement 2: I hereby give consent for my thesis, if accepted, to be available for photocopying and for inter-library loans after expiry of a bar on access approved by Aberystwyth University. Signature: Date 15/09/2020 1 Preface II. Summary Candidate’s Surname/Family Name Friedersdorff Candidate’s Forenames (in full) Jessica Charlotte Abigail Candidate for the Degree of PhD Academic year the work submitted for examination 2020 Summary: Greenhouse gas emissions and feed efficiency in ruminant livestock are pertinent and important topics, ones which have not suffered from lack of attention as ample research has endeavoured to further our understanding of the complex rumen microbial ecosystem.
    [Show full text]