Biochemistry and physiology of anaerobic bacteria

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Transcript of Biochemistry and physiology of anaerobic bacteria

Biochemistry and Physiology of Anaerobic Bacteria

SpringerNew YorkBerlinHeidelbergHong KongLondonMilanParisTokyo

Lars G. LjungdahlMichael W. Adams Larry L. BartonJames G. Ferry Michael K. Johnson

Editors

Biochemistry andPhysiology of Anaerobic Bacteria

With 71 Illustrations

13

Lars G. Ljungdahl Michael W. AdamsDepartment of Biochemistry and Department of Biochemistry and

Molecular Biology Molecular BiologyUniversity of Georgia University of GeorgiaAthens, GA 30602 Athens, GA 30602USA USAlarsljd@bmb.uga.edu adams@bmb.uga.edu

Larry L. Barton James G. FerryDepartment of Biology Department of Biochemistry andUniversity of New Mexico Molecular BiologyAlbuquerque, NM 87131 Pennsylvania State UniversityUSA University Park, PA 16801barton@unm.edu USA

Michael K. Johnsonjpf3@psu.edu

Department of ChemistryCenter for Metalloenzyme StudiesUniversity of GeorgiaAthens, GA 30602USAjohnson@chem.uga.edu

Library of Congress Cataloging-in-Publication DataBiochemistry and physiology of anaerobic bacteria / editors, Lars G. Ljungdahl . . . [et al.].

p. cm.Includes bibliographical references and index.ISBN 0-387-95592-5 (alk. paper)1. Anaerobic bacteria. I. Ljungdahl, Lars G.

QR89.5 .B55 2003579.3149dc21 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 scholarlyanalysis. 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, evenif the are not identied as such, is not to be taken as an expression of opinion as to whetheror 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 HeidelbergA member of BertelsmannSpringer Science+Business Media GmbH

To the memory of Harry D. Peck, Jr. (19271998)professor, founder, and chairman of theDepartment of Biochemistry at the University ofGeorgia and pioneer in studies of sulfate-reducingbacteria and hydrogenases.

Preface

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During the last thirty years, there have been tremendous advances withinall realms of microbiology. The most obvious are those resulting fromstudies using genetic and molecular biological methods. The sequencing ofwhole genomes of a number of microorganisms having different physiolo-gic properties has demonstrated their enormous diversity and the fact thatmany species have metabolic abilities previously not recognized. Sequenceshave also conrmed the division of prokaryotes into the domains ofArchaea and bacteria. Terms such as hyper- or extreme thermopiles, ther-mophilic alkaliphiles, acidophiles, and anaerobic fungi are now usedthroughout the microbial community. With these discoveries has come anew realization about the physiological and metabolic properties ofmicrooganisms. This, in turn, has demonstrated their importance for thedevelopment, maintenance, and sustenance of all life on Earth. Recent esti-mates indicate that the amount of prokaryotic biomass on Earth equalsand perhaps exceedsthat of plant biomass. The rate of uptake of carbonby prokaryotic microorganisms has also been calculated to be similar tothat of uptake of carbon by plants. It is clear that microorganisms playextremely 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 havemetabolic pathways only recently elucidated that enable them to use carbondioxide or carbon monoxide as the sole carbon source. Thus they are ableto grow autotrophically. These pathways differ from that of the classicalCalvin Cycle discovered in plants in the mid-1900s in that they lead to theformation of acetyl-CoA, rather than phosphoglycerate. The new pathwaysare prominent in several types of anaerobes, including methanogens, ace-togens, and sulfur reducers. It has been postulated that approximatelytwenty percent of the annual circulation of carbon on the Earth is by anaer-obic processes. That anaerobes carry out autotrophic type carbon dioxidexation prompted studies of the mechanisms by which they conserve energyand generate ATP. It is now clear that the pathways of autotrophic carbondioxide xation involve hydrogen metabolism and that they are coupled to

electron transport and generation of ATP by chemiosmosis. Enzymes catalyzing the metabolism of carbon dioxide, hydrogen, and other materialsfor building cell material and for electron transport are now intenselystudied in anaerobes. Almost without exception, these enzymes depend onmetals such as iron, nickel, cobalt, molybdenum, tungsten, and selenium.This pertains also to electron carrying proteins like cytochromes, severaltypes of iron-sulfur and avoproteins. Much present knowledge of electrontransport and phosphorylation in anaerobic microoganisms has beenobtained from studies of sulfate reducers. More recent investigations withmethanogens and acetogens corroborate the ndings obtained with thesulfate reducers, but they also demonstrate the diversity of mechanisms andpathways involved.

This book stresses the importance of anaerobic microorganisms in natureand relates their wonderful and interesting metabolic properties to the fas-cinating enzymes that are involved. The rst two chapters by H. Gest andH.G. Schlegel, respectively, review the recycling of elements and the diversity of energy resources by anaerobes. As mentioned above, hydrogenmetabolism plays essential roles in many anaerobes, and there are severaltypes of hydrogenase, the enzyme responsible for catalyzing the oxidationand production of this gas. Some contain nickel at their catalytic sites, inaddition 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 bySimon P.J. Albracht, and the activation of a puried hydrogenase fromDesulfovibrio 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 carbonmonoxide dehydrogenases, nitrogenases, many other reductases, and severaltypes of electron carrying proteins, is explored by J.N. Agar, D.R. Dean, andM.K. Johnson. R.J. Maier, J. Olson, and N. Mehta write about genes and pro-teins involved in the expression of nickel dependent hydrogenases. Genesand the genetic manipulations of Desulfovibrio are examined by J.D. Walland 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. Theyexplore the role of the hydrogenosome, which in the eukaryotic anaerobesreplaces the mitochondrion. A rather new aspect related to anerobicmicroorganisms is the observation that they exhibit some degree of toler-ance toward oxygen. They typically lack the known oxygen stress enzymessuperoxide dismutase and catalase, but they contain novel iron-containingprotein including hemerythrin-like proteins, desulfoferrodoxin, rubrery-thrin, new types of rubredoxins, and a new enzyme termed superoxidereductase. D.M. Kurtz, Jr., discuses in Chapter 10 these proteins and pro-poses that they function in the defense toward oxygen stress in anaerobes

viii Preface

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 acetateto acetyl-CoA, which is cleaved by acetyl-CoA synthase. The methyl groupis subsequently reduced to methane, and the carbonyl group is oxidized tocarbon dioxide. The pathway is similar but reverse of that of acetyl-CoAsynthesis by acetogens, but it involves cofactors unique to the methane-producing Archaea. Selenium has been found in several enzymes fromanaerobes including species of clostridia, acetogens, and methanogens. InChapter 12,W.T. Self has summarized properties of selenoenzymes, that aredivided into three groups. The rst constitutes amino acid reductases thatutilize glycine, sarcosine, betaine, and proline. In these and also in the secondgroup, which includes formate dehydrogenases, selenium is present asselenocysteine. Selenocysteine is incorporated into the polypeptide chainvia a special seryl-tRNA and selenophosphate. The third group of sele-noenzymes is selenium-molybdenum hydroxylases found in purinolyticclostridia. 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. Ksel highlight the diversity of acetogensand their ecological roles. A. Das and L.G. Ljungdahl discuss evidence thatthe acetyl-CoA pathway of carbon dioxide xation is coupled with electrontransport and ATP generation. In addition, they present some data showinghow acetogens can deal with oxydative stress. In Chapter 15, D.P. Kelly dis-cusses the biochemical features common to both anaerobic sulfate reducingbacteri