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Biochemistry and Physiology of Anaerobic Bacteria With 71 Illustrations 13 Lars G Ljungdahl Michael W Adams Department of Biochemistry and Department of Biochemistry and Molecular Biology Molecular Biology University of Georgia University of Georgia Athens GA 30602 Athens GA 30602 USA USA larsljd bmb uga edu adams bmb uga edu Larry L Barton James G Ferry Department of Biology Department
Biochemistry and,Physiology of,Anaerobic Bacteria,Heidelberg. Lars G Ljungdahl,Michael W Adams Larry L Barton,James G Ferry Michael K Johnson. Biochemistry and,Physiology of,Anaerobic Bacteria,With 71 Illustrations. Lars G Ljungdahl Michael W Adams, Department of Biochemistry and Department of Biochemistry and. Molecular Biology Molecular Biology,University of Georgia University of Georgia. Athens GA 30602 Athens GA 30602,USA USA,larsljd bmb uga edu adams bmb uga edu. Larry L Barton James G Ferry, Department of Biology Department of Biochemistry and. University of New Mexico Molecular Biology, Albuquerque NM 87131 Pennsylvania State University. USA University Park PA 16801,barton unm edu USA, jpf3 psu edu. Michael K Johnson,Department of Chemistry,Center for Metalloenzyme Studies. University of Georgia,Athens GA 30602,johnson chem uga edu. Library of Congress Cataloging in Publication Data. Biochemistry and physiology of anaerobic bacteria editors Lars G Ljungdahl et al . Includes bibliographical references and index , ISBN 0 387 95592 5 alk paper . 1 Anaerobic bacteria I Ljungdahl Lars G , QR89 5 B55 2003. 579 3 149 dc21 2002036546,ISBN 0 387 95592 5 Printed on acid free paper . 2003 Springer Verlag New York Inc , All rights reserved This work may not be translated or copied in whole or in part without. the written permission of the publisher Springer Verlag New York Inc 175 Fifth Avenue . New York NY 10010 USA except for brief excerpts in connection with reviews or scholarly. analysis Use in connection with any form of information storage and retrieval electronic. adaptation computer software or by similar or dissimilar methodology now known or here . after developed is forbidden , The use in this publication of trade names trademarks service marks and similar terms even. if the are not identi ed as such is not to be taken as an expression of opinion as to whether. or not they are subject to proprietary rights ,Printed in the United States of America . 9 8 7 6 5 4 3 2 1 SPIN 10893900,www springer ny com. Springer Verlag New York Berlin Heidelberg, A member of BertelsmannSpringer Science Business Media GmbH. To the memory of Harry D Peck Jr 1927 1998 ,professor founder and chairman of the. Department of Biochemistry at the University of, Georgia and pioneer in studies of sulfate reducing. bacteria and hydrogenases , During the last thirty years there have been tremendous advances within. all realms of microbiology The most obvious are those resulting from. studies using genetic and molecular biological methods The sequencing of. whole genomes of a number of microorganisms having different physiolo . gic properties has demonstrated their enormous diversity and the fact that. many species have metabolic abilities previously not recognized Sequences. have also con rmed the division of prokaryotes into the domains of. Archaea and bacteria Terms such as hyper or extreme thermopiles ther . mophilic alkaliphiles acidophiles and anaerobic fungi are now used. throughout the microbial community With these discoveries has come a. new realization about the physiological and metabolic properties of. microoganisms This in turn has demonstrated their importance for the. development maintenance and sustenance of all life on Earth Recent esti . mates indicate that the amount of prokaryotic biomass on Earth equals . and perhaps exceeds that of plant biomass The rate of uptake of carbon. by prokaryotic microorganisms has also been calculated to be similar to. that of uptake of carbon by plants It is clear that microorganisms play. extremely important and typically dominant roles in recycling and seques . tering of carbon and many other elements including metals . Many of the advances within microbiology involve anaerobes They have. metabolic pathways only recently elucidated that enable them to use carbon. dioxide or carbon monoxide as the sole carbon source Thus they are able. to grow autotrophically These pathways differ from that of the classical. Calvin Cycle discovered in plants in the mid 1900s in that they lead to the. formation of acetyl CoA rather than phosphoglycerate The new pathways. are prominent in several types of anaerobes including methanogens ace . togens and sulfur reducers It has been postulated that approximately. twenty percent of the annual circulation of carbon on the Earth is by anaer . obic processes That anaerobes carry out autotrophic type carbon dioxide. xation prompted studies of the mechanisms by which they conserve energy. and generate ATP It is now clear that the pathways of autotrophic carbon. dioxide xation involve hydrogen metabolism and that they are coupled to. viii Preface, electron transport and generation of ATP by chemiosmosis Enzymes. catalyzing the metabolism of carbon dioxide hydrogen and other materials. for building cell material and for electron transport are now intensely. studied in anaerobes Almost without exception these enzymes depend on. metals such as iron nickel cobalt molybdenum tungsten and selenium . This pertains also to electron carrying proteins like cytochromes several. types of iron sulfur and avoproteins Much present knowledge of electron. transport and phosphorylation in anaerobic microoganisms has been. obtained from studies of sulfate reducers More recent investigations with. methanogens and acetogens corroborate the ndings obtained with the. sulfate reducers but they also demonstrate the diversity of mechanisms and. pathways involved , This book stresses the importance of anaerobic microorganisms in nature. and relates their wonderful and interesting metabolic properties to the fas . cinating enzymes that are involved The rst two chapters by H Gest and. H G Schlegel respectively review the recycling of elements and the. diversity of energy resources by anaerobes As mentioned above hydrogen. metabolism plays essential roles in many anaerobes and there are several. types of hydrogenase the enzyme responsible for catalyzing the oxidation. and production of this gas Some contain nickel at their catalytic sites in. addition to iron sulfur clusters while others contain only iron sulfur clus . ters They also vary in the types of compounds that they use as electron car . riers The mechanism of activation of hydrogen by enzymes is discussed by. Simon P J Albracht and the activation of a puri ed hydrogenase from. Desulfovibrio vulgaris and its catalytic center by B Hanh Huynh P Tavares . A S Pereira I Moura and J G Moura The biosynthesis of iron sulfur clus . ters which are so prominent in most hydrogenases formate and carbon. monoxide dehydrogenases nitrogenases many other reductases and several. types of electron carrying proteins is explored by J N Agar D R Dean and. M K Johnson R J Maier J Olson and N Mehta write about genes and pro . teins involved in the expression of nickel dependent hydrogenases Genes. and the genetic manipulations of Desulfovibrio are examined by J D Wall. and her research associates In Chapter 8 G Voordouw discusses the func . tion and assembly of electron transport complexes in Desulfovibrio vulgaris . In the next chapter Richard Cammack and his colleagues introduce eukary . otic anaerobes including anaerobic fungi and their energy metabolism They. explore the role of the hydrogenosome which in the eukaryotic anaerobes. replaces the mitochondrion A rather new aspect related to anerobic. microorganisms is the observation that they exhibit some degree of toler . ance toward oxygen They typically lack the known oxygen stress enzymes. superoxide dismutase and catalase but they contain novel iron containing. protein including hemerythrin like proteins desulfoferrodoxin rubrery . thrin new types of rubredoxins and a new enzyme termed superoxide. reductase D M Kurtz Jr discuses in Chapter 10 these proteins and pro . poses that they function in the defense toward oxygen stress in anaerobes. Preface ix, and microaerophiles Over six million tons of methane is produced biolog . ically each year most of it from acetate by methanogenic anaerobes J G . Ferry describes in Chapter 11 that reactions include the activation of acetate. to acetyl CoA which is cleaved by acetyl CoA synthase The methyl group. is subsequently reduced to methane and the carbonyl group is oxidized to. carbon dioxide The pathway is similar but reverse of that of acetyl CoA. synthesis by acetogens but it involves cofactors unique to the methane . producing Archaea Selenium has been found in several enzymes from. anaerobes including species of clostridia acetogens and methanogens In. Chapter 12 W T Self has summarized properties of selenoenzymes that are. divided into three groups The rst constitutes amino acid reductases that. utilize glycine sarcosine betaine and proline In these and also in the second. group which includes formate dehydrogenases selenium is present as. selenocysteine Selenocysteine is incorporated into the polypeptide chain. via a special seryl tRNA and selenophosphate The third group of sele . noenzymes is selenium molybdenum hydroxylases found in purinolytic. clostridia The nature of the selenium in this group has yet to be determined . Chapters 13 and 14 deal with acetogens which produce anaerobically a tril . lion kilograms of acetate each year by carbon dioxide xation via the acetyl . CoA pathway H L Drake and K K sel highlight the diversity of acetogens. and their ecological roles A Das and L G Ljungdahl discuss evidence that. the acetyl CoA pathway of carbon dioxide xation is coupled with electron. transport and ATP generation In addition they present some data showing. how acetogens can deal with oxydative stress In Chapter 15 D P Kelly dis . cusses the biochemical features common to both anaerobic sulfate reducing. bacteria and aerobic thiosulfate oxidizing thiobacilli His chapter is also a. tribute to Harry Peck The last three chapters are devoted to the reduction. by anaerobic bacteria of metals metalloids and nonessential elements L L . Barton R M Plunkett and B M Thomson in their review point out the geo . chemical importance these reductions which involve both metal cations and. metal anions J Wiegel J Hanel and K Aygen describe the isolation of. recently discovered chemolithoautotrophic thermophilic iron III reducers. from geothermally heated sediments and water samples of hot springs They. propose that these bacteria are ancient and were involved in formation of. iron deposits during the Precambrian era The last chapter is a discussion of. electron ow in ferrous bioconversion by E J Laishley and R D Bryant . They visualize a model for biocorrosion by sulfate reducing bacteria. that involves both iron and nickel iron hydrogenases high molecular. cytochrome and electron transport using sulfate as an acceptor . Lars G Ljungdahl, Michael W Adams, Larry L Barton. James G Ferry, Michael K Johnson,Preface vii,Contributors xiii. 1 Anaerobes in the Recycling of Elements, in the Biosphere 1. Howard Gest, 2 The Diversity of Energy Sources of Microorganisms 11. Hans G nter Schlegel, 3 Mechanism of Hydrogen Activation 20. Simon P J Albracht, 4 Reductive Activation of Aerobically Puri ed Desulfovibrio. vulgaris Hydrogenase M ssbauer Characterization of the. Catalytic H Cluster 35, Boi Hanh Huynh Pedro Tavares Alice S Pereira . Isabel Moura and Jos J G Moura, 5 Iron Sulfur Cluster Biosynthesis 46. Jeffrey N Agar Dennis R Dean and Michael K Johnson. 6 Genes and Proteins Involved in Nickel Dependent. Hydrogenase Expression 67, R J Maier J Olson and N Mehta. 7 Genes and Genetic Manipulations of Desulfovibrio 85. Judy D Wall Christopher L Hemme Barbara Rapp Giles . Joseph A Ringbauer Jr Laurence Casalot and, Tara Giblin. xii Contents, 8 Function and Assembly of Electron Transport Complexes in. Desulfovibrio vulgaris Hildenborough 99, Gerrit Voordouw. 9 Iron Sulfur Proteins in Anaerobic Eukaryotes 113. Richard Cammack David S Horner Mark van der Giezen . Jaroslav Kulda and David Lloyd,10 Oxygen and Anaerobes 128. Donald M Kurtz Jr , 11 One Carbon Metabolism in Methanogenic Anaerobes 143. James G Ferry,12 Selenium Dependent Enzymes from Clostridia 157. William T Self, 13 How the Diverse Physiologic Potentials of Acetogens. Determine Their In Situ Realities 171, Harold L Drake and Kirsten K sel. 14 Electron Transport System in Acetogens 191, Amaresh Das and Lars G Ljungdahl. 15 Microbial Inorganic Sulfur Oxidation The APS Pathway 205. Donovan P Kelly,16 Reduction of Metals and Nonessential Elements. by Anaerobes 220, Larry L Barton Richard M Plunkett and. Bruce M Thomson, 17 Chemolithoautotrophic Thermophilic Iron III Reducer 235. Juergen Wiegel Justin Hanel and Kaya Aygen,18 Electron Flow in Ferrous Biocorrosion 252. E J Laishley and R D Bryant,Index 261, Contributors. Jeffrey N Agar, Department of Chemistry Center for Metalloenzyme Studies University of. Georgia Athens GA 30602 USA,Simon P J Albracht, Department of Biochemistry E C Slater Institute University of. Amsterdam NL 1018 TV Amsterdam The Netherlands,Kaya Aygen. Department of Microbiology Center for Biological Resource Recovery . University of Georgia Athens GA 30602 USA,Larry L Barton. Department of Biology University of New Mexico Albuquerque NM. 87131 USA,R D Bryant, Department of Biological Sciences University of Calgary Calgary Alberta. T2N lN4 Canada,Richard Cammack, Division of Life Sciences King s College London SE1 9NN UK. Laurence Casalot, Department of Biochemistry University of Missouri Columbia Columbia . MO 65211 USA,Amaresh Das, Department of Biochemistry and Molecular Biology Center for Biological. Resource Recovery University of Georgia Athens GA 30602 USA. xiv Contributors,Dennis R Dean, Department of Biochemistry Virginia Institute of Technology Blacksburg . VA 24061 USA,Harold L Drake, Department of Ecological Microbiology BITOEK University of Bayreuth . 95440 Bayreuth Germany,James G Ferry, Department of Biochemistry and Molecular Biology Pennsylvania State. University University Park PA 16801 USA,Howard Gest. Department of History and Philosophy of Science Department of Biology . Photosynthetic Bacteria Group Indiana University Bloomington IN. 47405 USA,Tara Giblin, 28024 Marguerite Parkway Mission Viejo CA 92692 USA. Justin Hanel, Department of Microbiology Center for Biological Resource Recovery . University of Georgia Athens GA 30602 USA,Boi Hanh Huynh. Department of Physics Emory University Atlanta GA 20322 USA. Christopher L Hemme, Department of Biochemistry University of Missouri Columbia Columbia . MO 65211 USA,David S Horner, Department of Zoology Molecular Biology Unit Natural History Museum . London SW7 5BD UK Current address Department of Physiology and. General Biochemistry University of Milan 20133 Milan Italy. Michael K Johnson, Department of Chemistry Center for Metalloenzyme Studies University of. Georgia Athens GA 30602 USA,Donovan P Kelly, Department of Biological Sciences University of Warwick Coventry CV4. Contributors xv,Jaroslav Kulda, Department of Parasitology Charles University 128 44 Prague 2 Czech. Donald M Kurtz Jr , Department of Chemistry Center for Metalloenzyme Studies University of. Georgia Athens GA 30602 USA,Kirsten K sel, Department of Ecological Microbiology BITOEK University of Bayreuth . 95440 Bayreuth Germany,E J Laishley, Department of Biological Sciences University of Calgary Calgary Alberta. T2N 1N4 Canada,Lars G Ljungdahl, Department of Biochemistry and Molecular Biology University of Georgia . Athens GA 30602 USA,David Lloyd, School of Pure and Applied Biology University of Wales Cardiff CF1 3TL . R J Maier, Department of Microbiology Center for Biological Resource Recovery . University of Georgia Athens GA 30602 USA, Department of Microbiology Center for Biological Resource Recovery . University of Georgia Athens GA 30602 USA,Isabel Moura. Departamento de Qu m ca e Centro de Qu m ca Fina e Biotecnologia . Faculdade de Ci ncias e Tecnologia Universidade Nova de Lisboa . 2825 114 Caparica Portugal,Jos J G Moura, Departamento de Qu m ca e Centro de Qu m ca Fina e Biotecnologia . Faculdade de Ci ncias e Tecnologia Universidade Nova de Lisboa . 2825 114 Caparica Portugal, Department of Microbiology Center for Biological Resource Recovery . University of Georgia Athens GA 30602 USA, xvi Contributors. Alice S Pereira, Departamento de Qu m ca e Centro de Qu m ca Fina e Biotecnologia . Faculdade de Ci ncias e Tecnologia Universidade Nova de Lisboa . 2825 114 Caparica Portugal,Richard M Plunkett, Department of Biology University of New Mexico Albuquerque NM. 87131 USA,Barbara Rapp Giles, Department of Biochemistry University of Missouri Columbia Columbia . MO 65211 USA,Joseph A Ringbauer Jr , Department of Biochemistry University of Missouri Columbia Columbia . MO 65211 USA,Hans G nter Schlegel, Institut f r Mikrobiologie der Georg August Universit t 37077 G ttingen . William T Self, Laboratory of Biochemistry National Heart Lung and Blood Institute . National Institutes of Health Bethesda MD 20892 USA . Pedro Tavares, Departamento de Qu m ca e Centro de Qu m ca Fina e Biotecnologia . Faculdade de Ci ncias e Tecnologia Universidade Nova de Lisboa . 2825 114 Caparica Portugal,Bruce M Thomson, Department of Civil Engineering University of New Mexico Albuquerque . NM 87131 USA,Mark van der Giezen, Department of Zoology Molecular Biology Unit Natural History Museum . London SW7 5BD UK Current address School of Biological Sciences . Royal Holloway University of London Egham Surrey TW2O OEX UK. Gerrit Voordouw, Department of Biological Sciences University of Calgary Calgary Alberta .