The Prokaryotes Eugene Rosenberg (Editor-in-Chief) Edward F DeLong, Stephen Lory, Erko Stackebrandt and Fabiano Thompson (Eds.) The Prokaryotes Prokaryotic Physiology and Biochemistry Fourth Edition With 220 Figures and 62 Tables Editor-in-Chief Eugene Rosenberg Department of Molecular Microbiology and Biotechnology Tel Aviv University Tel Aviv, Israel Editors Edward F DeLong Department of Biological Engineering Massachusetts Institute of Technology Cambridge, MA, USA Fabiano Thompson Laboratory of Microbiology, Institute of Biology, Center for Health Sciences Federal University of Rio de Janeiro (UFRJ) Ilha Funda˜o, Rio de Janeiro, Brazil Stephen Lory Department of Microbiology and Immunology Harvard Medical School Boston, MA, USA Erko Stackebrandt Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures Braunschweig, Germany ISBN 978-3-642-30140-7 ISBN 978-3-642-30141-4 (eBook) ISBN 978-3-642-30142-1 (print and electronic bundle) DOI 10.1007/978-3-642-30141-4 Springer Heidelberg New York Dordrecht London Library of Congress Control Number: 2012955034 3rd edition: © Springer Science+Business Media, LLC 2006 4th edition: © Springer-Verlag Berlin Heidelberg 2013 This work is subject to copyright All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed Exempted from this legal reservation are brief excerpts in connection with reviews or scholarly analysis or material supplied specifically for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work Duplication of this publication or parts thereof is permitted only under the provisions of the Copyright Law of the Publisher’s location, in its current version, and permission for use must always be obtained from Springer Permissions for use may be obtained through RightsLink at the Copyright Clearance Center Violations are liable to prosecution under the respective Copyright Law The use of general descriptive names, registered names, trademarks, service marks, etc in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use While the advice and information in this book are believed to be true and accurate at the date of publication, neither the authors nor the editors nor the publisher can accept any legal responsibility for any errors or omissions that may be made The publisher makes no warranty, express or implied, with respect to the material contained herein Printed on acid-free paper Springer is part of Springer ScienceỵBusiness Media (www.springer.com) Foreword The purpose of this brief foreword is unchanged from the first edition; it is simply to make you, the reader, hungry for the scientific feast that follows These 11 volumes (planned) on the prokaryotes offer an expanded scientific menu that displays the biochemical depth and remarkable physiological and morphological diversity of prokaryote life The size of the volumes might initially discourage the unprepared mind from being attracted to the study of prokaryote life, for this landmark assemblage thoroughly documents the wealth of present knowledge But in confronting the reader with the state of the art, the Handbook also defines where more work needs to be done on well-studied bacteria as well as on unusual or poorly studied organisms This edition of The Prokaryotes recognizes the almost unbelievable impact that the work of Carl Woese has had in defining a phylogenetic basis for the microbial world The concept that the ribosome is a highly conserved structure in all cells and that its nucleic acid components may serve as a convenient reference point for relating all living things is now generally accepted At last, the phylogeny of prokaryotes has a scientific basis, and this is the first serious attempt to present a comprehensive treatise on prokaryotes along recently defined phylogenetic lines Although evidence is incomplete for many microbial groups, these volumes make a statement that clearly illuminates the path to follow There are basically two ways of doing research with microbes A classical approach is first to define the phenomenon to be studied and then to select the organism accordingly Another way is to choose a specific organism and go where it leads The pursuit of an unusual microbe brings out the latent hunter in all of us The intellectual challenges of the chase frequently test our ingenuity to the limit Sometimes the quarry repeatedly escapes, but the final capture is indeed a wonderful experience For many of us, these simple rewards are sufficiently gratifying so that we have chosen to spend our scientific lives studying these unusual creatures In these endeavors, many of the strategies and tools as well as much of the philosophy may be traced to the Delft School, passed on to us by our teachers, Martinus Beijerinck, A J Kluyver, and C B van Niel, and in turn passed on by us to our students In this school, the principles of the selective, enrichment culture technique have been developed and diversified; they have been a major force in designing and applying new principles for the capture and isolation of microbes from nature For me, the ‘‘organism approach’’ has provided rewarding adventures The organism continually challenges and literally drags the investigator into new areas where unfamiliar tools may be needed I believe that organism-oriented research is an important alternative to problem-oriented research, for new concepts of the future very likely lie in a study of the breadth of microbial life The physiology, biochemistry, and ecology of the microbe remain the most powerful attractions Studies based on classical methods as well as modern genetic techniques will result in new insights and concepts To some readers, this edition of The Prokaryotes may indicate that the field is now mature, that from here on it is a matter of filling in details I suspect that this is not the case Perhaps we have assumed prematurely that we fully understand microbial life Van Niel pointed out to his students that—after a lifetime of study—it was a very humbling experience to view in the microscope a sample of microbes from nature and recognize only a few Recent evidence suggests that microbes have been evolving for nearly billion years Most certainly, those microbes now domesticated and kept in captivity in culture collections represent only a minor portion of the species that have evolved in this time span Sometimes we must remind ourselves that evolution is actively taking place at the present moment That the eukaryote cell evolved as a chimera of certain prokaryote parts is a generally accepted concept today Higher as well as lower eukaryotes evolved in contact with prokaryotes, and evidence surrounds us of the complex interactions between eukaryotes and prokaryotes as well as among prokaryotes We have so far only scratched the surface of these biochemical interrelationships Perhaps the legume nodule is a pertinent example of nature caught in the act of evolving the ‘‘nitrosome,’’ a unique nitrogen-fixing organelle The study of prokaryotes is proceeding at such a fast pace that major advances are occurring yearly The increase of this edition to four volumes documents the exciting pace of discoveries To prepare a treatise such as The Prokaryotes requires dedicated editors and authors; the task has been enormous I predict that the scientific community of microbiologists will again show its appreciation through use of these volumes—such that the pages will become ‘‘dog-eared’’ and worn as students seek basic information for the hunt These volumes belong in the laboratory, not in the library I believe that a most effective way to introduce students to microbiology is for them to isolate microbes from nature, that is, from their habitats in soil, water, clinical specimens, or plants The Prokaryotes enormously simplifies this process and should encourage the construction of courses that contain a wide spectrum of diverse topics For the student as well as the advanced investigator, these volumes should generate excitement Happy hunting! Ralph S Wolfe Department of Microbiology University of Illinois at Urbana-Champaign Preface During most of the twentieth century, microbiologists studied pure cultures under defined laboratory conditions in order to uncover the causative agents of disease and subsequently as ideal model systems to discover the fundamental principles of genetics and biochemistry Microbiology as a discipline onto itself, e.g., microbial ecology, diversity, and evolution-based taxonomy, has only recently been the subject of general interest, partly because of the realization that microorganisms play a key role in the environment The development and application of powerful culture-independent molecular techniques and bioinformatics tools has made this development possible The fourth edition of the Handbook of the Prokaryotes has been updated and expanded in order to reflect this new era of microbiology The first five volumes of the fourth edition contain 34 updated and 43 entirely new chapters Most of the new chapters are in the two new sections: Prokaryotic Communities and Bacteria in Human Health and Disease A collection of microorganisms occupying the same physical habitat is called a ‘‘community,’’ and several examples of bacterial communities are presented in the Prokaryotic Communities section, organized by Edward F DeLong Over the last decade, important advances in molecular biology and bioinformatics have led to the development of innovative culture-independent approaches for describing microbial communities These new strategies, based on the analysis of DNA directly extracted from environmental samples, circumvent the steps of isolation and culturing of microorganisms, which are known for their selectivity leading to a nonrepresentative view of prokaryotic diversity Describing bacterial communities is the first step in understanding the complex, interacting microbial systems in the natural world The section on Bacteria in Human Health and Disease, organized by Stephen Lory, contains chapters on most of the important bacterial diseases, each written by an expert in the field In addition, there are separate general chapters on identification of pathogens by classical and non-culturing molecular techniques and virulence mechanisms, such as adhesion and bacterial toxins In recognition of the recent important research on beneficial bacteria in human health, the section also includes chapters on gut microbiota, prebiotics, and probiotics Together with the updated and expanded chapter on Bacterial Pharmaceutical Products, this section is a valuable resource to graduate students, teachers, and researchers interested in medical microbiology Volumes 6–11, organized by Erko Stackebrandt and Fabiano Thompson, contain chapters on each of the ca 300 known prokaryotic families Each chapter presents both the historical and current taxonomy of higher taxa, mostly above the genus level; molecular analyses (e.g., DDH, MLSA, riboprinting, and MALDI-TOF); genomic and phenetic properties of the taxa covered; genome analyses including nonchromosomal genetic elements; phenotypic analyses; methods for the enrichment, isolation, and maintenance of members of the family; ecological studies; clinical relevance; and applications As in the third edition, the volumes in the fourth edition are available both as hard copies and e-books, and as eReferences The advantages of the online version include no restriction of color illustrations, the possibility of updating chapters continuously and, most importantly, libraries can place their subscribed copies on their servers, making it available to their community in offices and laboratories The editors thank all the chapter authors and the editorial staff of Springer, especially Hanna Hensler-Fritton, Isabel Ullmann, Daniel Quin˜ones, Alejandra Kudo, and Audrey Wong, for making this contribution possible Eugene Rosenberg Editor-in-Chief About the Editors Eugene Rosenberg (Editor-in-Chief) Department of Molecular Microbiology and Biotechnology Tel Aviv University Tel Aviv Israel Eugene Rosenberg holds a Ph.D in biochemistry from Columbia University (1961) where he described the chemical structures of the capsules of Hemophilus influenzae, types B, E, and F His postdoctoral research was performed in organic chemistry under the guidance of Lord Todd in Cambridge University He was an assistant and associate professor of microbiology at the University of California at Los Angeles from 1962 to 1970, where he worked on the biochemistry of Myxococcus xanthus Since 1970, he has been in the Department of Molecular Microbiology and Biotechnology, Tel Aviv University, as an associate professor (1970–1974), full professor (1975–2005), and professor emeritus (2006–present) He has held the Gol Chair in Applied and Environmental Microbiology since 1989 He is a member of the American Academy of Microbiology and European Academy of Microbiology He has been awarded a Guggenheim Fellowship, a Fogarty International Scholar of the NIH, the Pan Lab Prize of the Society of Industrial Microbiology, the Proctor & Gamble Prize of the ASM, the Sakov Prize, the Landau Prize, and the Israel Prize for a ‘‘Beautiful Israel.’’ His research has focused on myxobacteriology; hydrocarbon microbiology; surface-active polymers from Acinetobacter; bioremediation; coral microbiology; and the role of symbiotic microorganisms in the adaptation, development, behavior, and evolution of animals and plants He is the author of about 250 research papers and reviews, books, and 16 patents x About the Editors Edward F DeLong Department of Biological Engineering Massachusetts Institute of Technology Cambridge, MA USA Edward DeLong received his bachelor of science in bacteriology at the University of California, Davis, and his Ph.D in marine biology at Scripps Institute of Oceanography at the University of California, San Diego He was a professor at the University of California, Santa Barbara, in the Department of Ecology for years, before moving to the Monterey Bay Aquarium Research Institute where he was a senior scientist and chair of the science department, also for years He now serves as a professor at the Massachusetts Institute of Technology in the Department of Biological Engineering, where he holds the Morton and Claire Goulder Family Professorship in Environmental Systems DeLong’s scientific interests focus primarily on central questions in marine microbial genomics, biogeochemistry, ecology, and evolution A large part of DeLong’s efforts have been devoted to the study of microbes and microbial processes in the ocean, combining laboratory and field-based approaches Development and application of genomic, biochemical, and metabolic approaches to study and exploit microbial communities and processes is his another area of interest DeLong is a fellow in the American Academy of Arts and Science, the U.S National Academy of Science, and the American Association for the Advancement of Science 648 18 Physiology and Biochemistry of the Methane-Producing Archaea Na+ MtrE CM MtrC Cytoplasma MtrD D MtrG MtrA MtrB MtrF S Co CH3-H4MPT O Zn2+ S R N SO3– H3C N HN H2N CH3 H N SO3– H-S-CoM H CH3-S-CoM N MtrH H O H4MPT H N R N HN H2N H N N H Fig 18.11 Model of the methyl-H4MPT:CoM-SH methyltransferase complex A conserved aspartate residue (D) predicted to be located in a transmembrane helix of subunit MtrE is highlighted This residue could be essential for sodium ion translocation (Modified from Gottschalk and Thauer (2001)) the protein as an axial ligand (Harms and Thauer 1997; > Fig 18.12) Binding of this axial ligand could therefore be associated with a conformational change of the protein Upon demethylation of the cobamide, the axial ligand would be lost, and the conformational change would be reversed Since demethylation is Na+ dependent, the conformational change associated with this step can be coupled with the vectorial translocation of Na+ The MtrH subunit can be separated from the MtrA-H-complex The isolated MtrH subunit can catalyze the methylation of free cob(I)amide with methyl-H4MPT (Hippler and Thauer 1999) Therefore, MtrH is thought to catalyze the methylation of the corrinoid prosthetic group, which is bound to MtrA Subunit MtrE is thought to transfer the methyl group from the corrinoid prosthetic group of MtrA to coenzyme M, which is the Na+-dependent reaction (Gottschalk and Thauer 2001) MtrE is predicted to form six transmembrane spanning helixes and to have a large cytoplasmic domain containing a typical zinc-binding motif All enzymes known to date that catalyze the alkylation of a thiol group are zinc proteins The reaction catalyzed by N5-methyl-H4MPT:CoMSH methyltransferase is analogous to the formation of Unmethylated MtrA Methylated MtrA CH3-H4MPT H4MPT CH3 MtrH Co3+ MtrE ? His Co1+ His CH3-s-CoM H-s-CoM Na+ Fig 18.12 Proposed conformational change of subunit MtrA of the methylH4MPT:CoM-SH methyltransferase complex upon methylation and demethylation of its corrinoid prosthetic group The MtrH subunit is proposed to catalyze the methylation of the cobamide bound to MtrA The demethylation reaction is thought to be catalyzed by MtrE and coupled with vectorial sodium ion translocation since this reaction is sodium ion dependent (Modified from Gottschalk and Thauer (2001)) Physiology and Biochemistry of the Methane-Producing Archaea methionine from N5-methyl-H4F and homocysteine, which is catalyzed by methionine synthase (Banerjee et al 1989) However, methionine synthase is a soluble enzyme containing only one type of subunit, reflecting the fact that the methyl transfer to homocysteine is not coupled to energy conservation Activation of Methanol and Methylamines As shown in > Fig 18.13, methylotrophic methanogenesis begins with the transfer of the methyl group from a variety of substrates to coenzyme M For each substrate, there is a different methyltransferase system, specific for methanol (Mta), monomethylamine (Mtm), dimethylamine (Mtb), trimethylamine (Mtt), tetramethylammonium (Mtq), and methylthiols (Mts; Thauer and Sauer 1999; Ferguson et al 2000) Each system is composed of two methyltransferases, designated ‘‘MT1’’ (MtaB, MtmB, MtbB, MttB, and MtqB) and ‘‘MT2’’ (MtaA, MtbA, and MtqA), and a substrate-specific methylotrophic corrinoid protein (MtaC, MtmC, MtbC, MttC, and MtqC) containing a modified cobamide MT1 in each system catalyzes the methylation of the reduced corrinoid protein, and MT2 catalyzes the transfer of the methyl group from the corrinoid protein to coenzyme M Only in dimethylsulfide:coenzyme M methyltransferase are both methyl transfer reactions catalyzed by the same subunit (MtsA; Tallant et al 2001) The MT2 proteins have high sequence similarity and contain zinc in the active site Likewise, the sequences of the corrinoid proteins are related, all exhibiting a corrinoid-binding motif In contrast, the substrate-activating MT1 enzymes are not phylogenetically related For instance, MtaB, which activates methanol, is a zinc protein, but the other methylamine methyltransferases are not (Sauer and Thauer 1997) The genes encoding MtmB, MtbB, and MttB contain a single conserved in-frame amber codon (UAG) that is read through during translation (James et al 2001) In the structure of MtmB, the UAG-encoded residue was identified as a lysine in amide linkage to (4R, 5R)-4-substituted-pyrroline-5-carboxylate (called ‘‘pyrrolysine’’; Hao et al 2002) Furthermore, an amber-decoding tRNA was identified (Srinivasan et al 2002) Pyrrolysine can therefore be regarded as the twenty-second genetically encoded amino acid Pyrrolysine is thought to position the methyl group of methylamine for attack by the corrinoid protein (Hao et al 2002) The Aceticlastic Reaction Species of Methanosarcina, as well as those of Methanosaeta, grow during the catabolism of acetate to CO2 and CH4 (Ferry 1997) This is the acetate cleavage or aceticlastic reaction, where methane is formed without oxidation of the methyl group of acetate Instead, after activation to acetyl-CoA, the acetyl C-C bond is cleaved by the multienzyme complex of acetyl-CoA synthase and carbon monoxide dehydrogenase (Acs/CODH), which in Methanosarcina barkeri and Methanosarcina thermophila is composed of five different subunits (a subunit, CdhA; b subunit, CdhC; g subunit, CdhE; d subunit, CdhD; and subunit, CdhB) The overall reaction catalyzed by the CH3-S-CoM H-S-CoM H2O Methanol MMS Co MtsA MtaA MtaC DMS Co MtaB MtsB NH4+ MtbA MtqA Co MtqC MtmC MMA 18 MtbA MtaA/ MtbA MtmB MMA MttC Co Co MtbC Co TMA MtqB DMA QMA DMA MttB MtbB TMA Fig 18.13 Enzymes involved in the formation of methyl-coenzyme M from methanol, monomethylamine (MMA), dimethylamine (DMA), trimethylamine (TMA), tetramethylammonium (QMA), and dimethylsulfide (DMS) Except for DMS, the B subunits transfer the methyl groups from the substrates to the corrinoid prosthetic groups of the C subunits The A subunits then transfer the methyl groups from the corrinoid to CoM-SH For DMS, the A subunit catalyzes both transfers Abbreviations: MMS, methanethiol; Co, corrinoid prosthetic group 649 650 18 Physiology and Biochemistry of the Methane-Producing Archaea complex is the conversion of acetyl-CoA and tetrahydrosarcinapterin (H4SPT) to CO2, N5-methyl-tetrahydrosarcinapterin (CH3-H4SPT), CoA-SH, and reducing equivalents (reaction 5) Tetrahydrosarcinapterin is similar in structure and function to tetrahydromethanopterin, which is common in the hydrogenotrophic methanogens CH3COO− ATP CH3CO~SCoA H4SPT Fdox + − Acetyl CoA ỵ H4 SPT ỵ H2 O ỵ 2Fdox $ CoA SH ỵ CH3 H4 SPT ỵ CO2 þ 2FDred þ 2Hþ Acs/CODH ð18:5Þ A ferredoxin was identified as the physiological electron acceptor In autotrophic methanoarchaea and the homoacetogenic bacteria like Moorella thermoacetica, a homologous enzyme system functions in the reverse direction for the biosynthesis of acetyl-CoA This overall reaction is made up of a series of partial reactions catalyzed by different protein subcomponents of the complex (Abbanat and Ferry 1991; Grahame and DeMoll 1996) The b subunit, the recombinant form of which can be produced in Escherichia coli, reacts with acetyl-CoA to form an acetylenzyme intermediate Furthermore, this subunit catalyzes the formation of acetyl-CoA from CoA-SH, CO, and methylcobalamin in the absence of other Acs/CODH subunits, demonstrating that this subunit catalyzes the reversible C–C bond activation (Gencic and Grahame 2003) The b subunit also harbors the ‘‘A-cluster,’’ which contains a Ni-Ni-[4Fe-4S] site, as deduced from the crystal structures of Acs/CODH from Moorella thermoacetica (Darnault et al 2003; Seravalli et al 2004) and Carboxydothermus hydrogenoformans (Svetlitchnyi et al 2004) The CO generated in the C–C cleavage reaction is transferred via a gas channel to the site of the CO dehydrogenase activity, which is on the a subcomplex The isolated a subcomplex catalyzes the oxidation of CO to CO2 Furthermore, the sequence of the a subunit is related to the sequences of the much simpler CO dehydrogenases from Rhodospirillum rubrum and Carboxydothermus hydrogenoformans The active site of CO dehydrogenase also contains a Ni-Fe/S center, which could be either a [Ni-Fe4-S4] or a [Ni-Fe4-S5] center, as deduced from the crystal structure of these enzymes (Dobbek et al 2001; Drennan et al 2001) The methyl group generated in the b subunit is transferred to the corrinoid cofactor present in the gd subcomplex, which catalyzes the subsequent methyl transfer to the substrate H4SPT Here, the methyl group enters the general methanogenic pathway, which leads to the formation of CH4 (> Fig 18.2) Reducing equivalents required for the reduction of the heterodisulfide are provided by reduced ferredoxin formed in the CO dehydrogenase reaction There might be alternative electron transport chains to couple ferredoxin oxidation to heterodisulfide reduction In Methanosarcina barkeri, H2 is thought to be an intermediate in this electron transfer reaction This conclusion is based on several observations First, H2 accumulates during growth on acetate Second, acetate-grown cells have high levels of the Ech CO2 + CoA ΔμH+ ? Ech Fdred 2H+ H2 H2 CH3-H4SPT Vho CH3-CoM H-S-CoM MPH2 H+ MP H-S-CoB Hdr CoM-S-S-CoB +2H+ CH4 Fig 18.14 Pathway of methanogenesis from acetate in Methanosarcina barkeri Recent data indicate that the [4Fe-4S] ferredoxin (Fd) from M barkeri mediates electron transfer between acetyl-CoA synthase/CO dehydrogenase (Acs/CODH) and Ech hydrogenase Abbreviations: CH3-H4SPT, methyl-tetrahydrosarcinapterin; MP, methanophenazine; MPH2, reduced methanophenazine hydrogenase and methanophenazine-reducing hydrogenase Third, Ech hydrogenase is essential for growth of M barkeri on acetate It has therefore been proposed that this enzyme catalyzes H2 formation from reduced ferredoxin (Meuer et al 2002) H2 thus formed could then diffuse to the extracytoplasmic side of the membrane, where it becomes oxidized by the methanophenazine-reducing hydrogenase Reduced methanophenazine is then the electron donor for the heterodisulfide reductase (> Fig 18.14) On the other hand, M acetivorans forms methane from acetate but lacks a functional Ech hydrogenase (Galagan et al 2002) Hence, there must exist an alternative route to channel electrons from reduced ferredoxin into a membranebound electron transport chain that leads to heterodisulfide reduction The Hydrogenases of Methanoarchaea: A Summary For most methanoarchaea, methanogenesis from H2 and CO2 is the only way to obtain energy for growth Also growth on acetate could involve H2 formation and H2 consumption as discussed above Therefore, hydrogenases are essential enzymes for methanoarchaea, which is reflected by the presence of Physiology and Biochemistry of the Methane-Producing Archaea five different types of hydrogenases in these organisms Four of these enzymes are [NiFe]À hydrogenases, and one enzyme is an iron-sulfur cluster-free hydrogenase that has only been found in methanoarchaea Methanoarchaea seem to be lacking [FeFe] hydrogenases For a more detailed description of hydrogenases including those from methanoarchaea, see > Chap 4, ‘‘H2-Metabolizing Prokaryotes’’ in this volume F420-Reducing Hydrogenase This enzyme (Frh) is conserved in all methanoarchaea studied Some organisms contain two closely related isoenzymes The enzyme catalyzes the reduction of the deazaflavin coenzyme F420 and thus provides the reducing equivalents for the two intermediate reduction steps of the C1 pathway Frh is a soluble [NiFe] hydrogenase composed of three subunits, including the ‘‘hydrogenase large subunit’’ and the ‘‘hydrogenase small subunit’’ that form the basic module of all [NiFe] hydrogenases The third subunit contains iron-sulfur clusters and FAD It is assumed to harbor the F420-binding site (Sorgenfrei et al 1997) H2-Forming Methylene-H4MPT Dehydrogenase As outlined above, all hydrogenotrophic methanogens possess an F420-dependent dehydrogenase for the reduction of methenyl-H4MPT Reduction of F420 to F420H2 by H2 is catalyzed by Frh Methanoarchaea belonging to the orders Methanobacteriales, Methanococcales, and Methanopyrales also possess an enzyme that directly reduces methenyl-H4MPT to methylene-H4MPT using H2 as the electron donor (Thauer et al 1996; > Fig 18.15) Because this enzyme oxidizes H2, it is a hydrogenase by definition However, because this reaction is so unusual, it has been called the ‘‘H2-forming methylene-H4MPT dehydrogenase’’ (Hmd) In contrast to the well-characterized [NiFe] hydrogenases and [FeFe] hydrogenases, Hmd does not contain Ni or iron-sulfur clusters The primary sequence of Hmd does not possess similarity to known proteins O + N H2N N pro-R pro-S H O N Hmd H N Furthermore, the enzyme is not inhibited by CO at concentrations known to inhibit other hydrogenases, and it does not catalyze the reduction of redox dyes such as benzyl- or methylviologen It does catalyze the exchange between H2 and protons and the conversion of para H2 to ortho H2 but only in the presence of methenyl-H4MPT More detailed mechanistic studies have shown that the enzyme catalyzes the reversible reduction of methenyl-H4MPT to methylene-H4MPT in a ternary complex catalytic mechanism In this reaction, a hydride is transferred from H2 into the pro-R position at C14 of methenyl-H4MPT Iron at concentrations up to mol of Fe per mol of enzyme is the only metal that has been detected in Hmd This iron was not redox active and not considered to be functional The enzyme was therefore called ‘‘metal-free’’ hydrogenase Recently, active enzyme was shown to contain a cofactor (Buurman et al 2000) Addition of the purified cofactor to the apoprotein, which can be produced in E coli, resulted in active enzyme The structure of the active cofactor is not yet known But upon illumination with ultraviolet (UV)-A/blue light, the cofactor is inactivated and Fe and CO are released (Lyon et al 2004b) The remaining organic component could be cleaved by phosphodiesterase to GMP and a pyridone moiety, which is a new structure in biology (Shima et al 2004) How this organic compound is involved in iron complexation in the active Hmd cofactor remains to be shown There is experimental evidence that two CO are bound to the iron center (Lyon et al 2004a) Interestingly, CO is also a ligand to the iron center in [NiFe]À and [FeFe]À hydrogenases In cells cultivated under Ni-limiting conditions, the [NiFe] hydrogenase Frh is barely detectable, while the concentration of Hmd in the cell increases (Afting et al 1998) Hmd in combination with F420-dependent methylene-H4MPT dehydrogenase (Mtd) mediates the reduction of coenzyme F420 by H2 and thus provides an alternative source for reduced coenzyme F420 This allows the cell to spare Ni In contrast to the [NiFe] hydrogenase, Frh, Hmd, and Mtd are not oxygen sensitive This becomes important in the context of the recent finding that methanoarchaea contain an F420H2 oxidase, which catalyzes the reduction of O2 to H2O with F420H2 as the electron donor (Seedorf et al 2004) The reduction of O2 with H2 in H N N H CH3 + H2 CH3 Methenyl-H4MPT 18 H2N CH3+ H+ N N N N N H CH3 Methylene-H4MPT Fig 18.15 Reaction catalyzed by H2-forming methylene-H4MPT dehydrogenase (Hmd) In the presence of H2, methenyl-H4MPT is reduced to methylene-H4MPT 651 652 18 Physiology and Biochemistry of the Methane-Producing Archaea methanoarchaea is not coupled with energy conservation The function of this oxidase is most probably to reduce the intracellular O2 concentration to a level that allows growth and methanogenesis There is evidence that the O2 concentration has to be lowered well below mM in order for a ‘‘nanaerobe’’ to grow (Baughn and Malamy 2004) The function of F420H2 oxidase is, therefore, O2 detoxification F420-Nonreducing Hydrogenase F420-nonreducing hydrogenase (Mvh) is a soluble [NiFe] hydrogenase In addition to the basic hydrogenase module of two subunits, the enzyme contains a third subunit, a 17-kDa protein that carries a [2Fe-2S] cluster In M marburgensis, Mvh forms an enzyme complex with heterodisulfide reductase (Hdr) There is indirect evidence that the hydrogenase interacts via its 17-kDa subunit with Hdr (Stojanowic et al 2003) This type of hydrogenase is not found in Methanosarcina species Methanophenazine-Reducing Hydrogenases Methanosarcina species form two closely related [NiFe] hydrogenases, encoded by the vho and the vht transcriptional units In addition to the basic hydrogenase module, these enzymes contain a membrane-anchoring b-type cytochrome, which easily becomes separated from the hydrogenase module during purification These enzymes possess the highest similarity to the membrane-bound, periplasmically oriented uptake hydrogenases of bacteria (Vignais et al 2001) Vho and vht also contain a twin arginine leader peptide in their hydrogenase small subunit, indicating that the hydrophilic subunits of these enzymes are translocated across the membrane by twin arginine translocation (TAT) machinery This type of hydrogenase has only been found in Methanosarcina species where it is part of the H2:CoM-S-S-CoB oxidoreductase system (Deppenmeier et al 1999; > Fig 18.5) The vhoGAC operon is expressed during growth on H2/CO2, methanol, or acetate The vhtGAC operon is only expressed during growth on H2/CO2 and methanol but not during growth on acetate (Deppenmeier 1995) Whether this pattern of expression reflects a different metabolic function is not known Energy-Converting [NiFe] Hydrogenases Energy-converting [NiFe] hydrogenase (Ech) is an integral membrane protein, which, when purified, is composed of six subunits, corresponding to the products of the echABCDEF operon (Kaănkel et al 1998; Meuer et al 1999) Ech hydrogenase is only distantly related to the other [NiFe] hydrogenases found in methanoarchaea The subunits of this enzyme are closely related to members of a small group of membrane-bound [NiFe] hydrogenases, such as hydrogenase from E coli and the CO-induced hydrogenase from Rhodospirillum rubrum The sequences of the six subunits conserved in these enzymes are closely related to subunits present in the central part of complex I from mitochondria and bacteria (Hedderich 2004) The EchA and EchB subunits of the enzyme are predicted to be membrane-spanning proteins, while the other four subunits are expected to extrude into the cytoplasm A low-potential, soluble two [4Fe-4S] ferredoxin (E00 = À420 mV) isolated from M barkeri was identified as the electron donor/acceptor of Ech As outlined above, this enzyme provides the cell with reduced ferredoxin required for the first step of methanogenesis and for certain anabolic reactions In vivo, the reduction of the ferredoxin by H2 is thought to be driven by reversed electron transport In aceticlastic methanogenesis, Ech was proposed to catalyze the reverse reaction (i.e., the production of H2 with reduced ferredoxin as electron donor) This has been concluded from experiments with intact cells Cell suspensions of wild-type M barkeri convert CO quantitatively to CO2 and H2 Cell suspensions of the Dech mutant catalyzed the oxidative half of the aceticlastic pathway (conversion of CO to CO2 and H2) at a significantly lower rate than the wild type, indicating that Ech is the hydrogenase involved in this reaction (Meuer et al 2002) Importantly, the conversion of CO to CO2 and H2 in wild-type M barkeri was found to be coupled to the generation of a proton motive force This is consistent with the putative ion-translocating activity of Ech Ech hydrogenase thus far has only been purified from Methanosarcina species The genomes of Methanothermobacter thermautotrophicus, Methanococcus jannaschii, and Methanopyrus kandleri not encode a homologue of the sixsubunit Ech hydrogenase present in Methanosarcina However, these organisms encode related enzymes, which are predicted to have a much more complex subunit architecture (> Fig 18.16) Methanothermobacter thermautotrophicus, M marburgensis, and M jannaschii each encode two hydrogenases of this type, designated ‘‘Eha’’ and ‘‘Ehb’’ (Tersteegen and Hedderich 1999) Methanopyrus kandleri only encodes for one of these hydrogenases (Slesarev et al 2002) In M marburgensis, the length of the transcription units was determined The eha operon (12.5 kb) and the ehb operon (9.6 kb) were found to be composed of 20 and 17 ORFs, respectively Sequence analysis of the deduced proteins indicated that the eha and ehb operons each encode a [NiFe] hydrogenase large subunit, a [NiFe] hydrogenase small subunit, and two conserved integral membrane proteins These proteins show high sequence similarity to subunits of Ech hydrogenase from Methanosarcina barkeri In addition to these four subunits, the eha operon encodes a 6[4Fe-4S] polyferredoxin, a 10[4F-4S] polyferredoxin, four nonconserved hydrophilic subunits, and ten nonconserved integral membrane proteins; the ehb operon encodes a 2[4Fe-4S] ferredoxin, a 14[4Fe-4S] polyferredoxin, two nonconserved hydrophilic subunits, and nine nonconserved integral membrane proteins Since Methanothermobacter species only grow with H2/CO2 as energy substrates, it has been proposed that these membrane-bound [NiFe] hydrogenases catalyze the reduction of a low-potential ferredoxin or polyferredoxins by H2 in a reaction driven by Physiology and Biochemistry of the Methane-Producing Archaea Ech hydrogenase ech A B C D E F H I J 18 M barkeri Eha hydrogenase eha A B C D E F G KL M N O P Q R S T M marburgensis Ehb hydrogenase ehb A B C D E F G H I J K L M N O P Q M marburgensis = hydrogenase large subunit = hydrogenase small subunit; × [4Fe-4S] = electron-transfer protein; n × [4Fe-4S] = integral membrane protein ( = conserved integral membrane protein) = non-conserved hydrophilic protein Fig 18.16 Organization of the Methanosarcina barkeri ech operon and the Methanothermobacter marburgensis eha and ehb operons Abbreviations: [4Fe-4S], iron-sulfur cluster; n x [4Fe-4S], polyferredoxin encoded by the operon reversed electron transport, in analogy to the function of Ech hydrogenase in M barkeri when the organism is cultivated on H2/CO2 A purification of these enzymes has not been achieved thus far Methanogenic Coenzymes and Enzymes in Nonmethanogenic Archaea and Bacteria Sulfate-Reducing Archaea Use Three Methanogenic Coenzymes for the Oxidation of Reduced C1 Compounds to CO2 So far, all isolated archaeal sulfate reducers belong to the genus Archaeoglobus The best-studied species is Archaeoglobus fulgidus, for which the genome sequence is also known (Klenk et al 1997) Archaeoglobus fulgidus couples the oxidation of lactate to CO2 with the reduction of sulfate to H2S Lactate is first oxidized to pyruvate, which is subsequently converted to acetyl-CoA, CO2, and 2[H] Cleavage of the C–C-bond of acetyl-CoA is catalyzed by the Acs/CODH complex, which has the same subunit architecture and high sequence similarity to the enzyme from methanoarchaea (Dai et al 1998) This reaction generates enzyme-bound CO, which is oxidized to CO2, and an enzyme-bound methyl group For the oxidation of the methyl group to CO2, A fulgidus uses three coenzymes characteristic of the methanoarchaea: tetrahydromethanopterin, methanofuran, and coenzyme F420 (Moăller-Zinkhan et al 1989; Gorris et al 1991) The methyl group is first transferred to H4MPT and then stepwise oxidized to CO2 by the same reactions and enzymes found in methanoarchaea (> Fig 18.2) The F420H2 formed in this oxidative pathway is reoxidized by a membrane-bound F420H2 dehydrogenase, which closely resembles the enzyme from Methanosarcina species (Kunow et al 1994; Klenk et al 1997) Archaeoglobus fulgidus contains a modified menaquinone, which probably functions as the electron acceptor of this dehydrogenase It is not yet clear how electrons are transferred from the menaquinone pool to the enzymes of sulfate reduction Recently, a membrane-bound menaquinol-acceptor oxidoreductase that might mediate the electron transfer from the menaquinone pool to an as yet unidentified electron carrier in the cytoplasm has been isolated (Mander et al 2002) The sequences of two of the subunits of this enzyme are related to those of the heterodisulfide reductase from Methanosarcina species, including the catalytic subunit of Hdr However, Archaeoglobus lacks coenzymes M and B Therefore, this heterodisulfide-reductase-like enzyme has been proposed to catalyze the reduction of an unidentified disulfide substrate, which in turn could function as an electron donor of the enzymes of sulfate reduction, such as APS reductase and sulfite reductase Tetrahydromethanopterin-Dependent Formaldehyde Oxidation in Methylotrophic Bacteria In the metabolism of aerobic methylotrophic bacteria, formaldehyde is formed as a central intermediate from various C1 substrates Different pathways of formaldehyde oxidation to CO2 are known, one being tetrahydromethanopterin dependent The H4MPT-dependent pathway was first discovered in Methylobacterium extorquens This organism, in addition to the tetrahydrofolate-dependent pathway, has an H4MPT-dependent route for formaldehyde oxidation, which is now believed to be the main catabolic route in this organism (Chistoserdova et al 1998) The pathway involves three H4MPT-dependent steps, which are catalyzed by an NADH-dependent methyleneH4MPT dehydrogenase, a methenyl-H4MPT cyclohydrolase, and a formyltransferase/hydrolase complex H4MPT-dependent enzymes have also been detected in many other methylotrophic proteobacteria For a more detailed review, see > Chap 7, ‘‘Aerobic Methylotrophic Prokaryotes’’ in this volume 653 654 18 Physiology and Biochemistry of the Methane-Producing Archaea F420 in Nonmethanogenic Organisms Coenzyme F420 was first discovered in methanogenic archaea Later, coenzyme F420 was also identified in Archaeoglobus, Mycobacterium, Nocardia, Streptomyces, cyanobacteria, and some eukaryotes (Choi et al [2001] and literature cited therein) The role of F420 in Archaeoglobus is similar to that in methanogens Coenzyme F420 is used by Streptomyces species for tetracycline and lincomycin biosynthesis and may be used in mitomycin C biosynthesis In Mycobacterium and Nocardia species, coenzyme F420 is used by a coenzyme F420-dependent glucose-6-phosphate dehydrogenase Enzymes belonging to the deazaflavin class of photolyases, which are found in the green alga Scenedesmus and the cyanobacterium Synechocystis, contain 8-hydroxyazoriboflavin (also called ‘‘coenzyme F0’’) Coenzyme F420 is a derivative of coenzyme F0 CoM-SH in Bacterial Aliphatic Epoxide Carboxylation Until 1999, methanoarchaea were the only organisms known to possess coenzyme M, which is the smallest organic cofactor found in nature It was then discovered that coenzyme M also plays an essential role in the bacterial metabolism of short-chain epoxyalkanes, as revealed by initial studies with Xanthobacter autotrophicus and Rhodococcus rhodochrous (Allen et al 1999) These organisms use coenzyme M as the nucleophile for the epoxide ring opening, which results in the formation of the thioether bond between CoM-SH and a 2-hydroxyalkyl residue After oxidation to the corresponding 2-ketoalkyl-CoM intermediate, the thioether bond is attacked by a cysteine residue present in the active site of one of the key enzymes of the pathway This results in the formation of a mixed disulfide between CoM-SH and the active-site cysteine and a carbanion, which becomes carboxylated Reduction of the mixed disulfide in an NADH-dependent step regenerates coenzyme M Coenzyme M seems to be ideally suited as a nucleophile and carrier molecule in this pathway (reviewed in Ensign and Allen 2003) Do Anaerobic Methane Oxidizers Use the Methanogenic Pathway in Reverse? Although the elucidation of the pathway of CO2 reduction in methanogens required the discovery of a large number of novel coenzymes and enzymatic reactions, many of these catalysts were subsequently found in other organisms For many years, the reaction catalyzed by methyl-coenzyme M reductase seemed to be the only step of the pathway that was truly unique to the methanoarchaea However, very recently, genes encoding a methyl-coenzyme M reductase-like enzyme were identified in habitats where methane-oxidizing microbial communities are abundant (Hallam et al 2003) From the biomass of one of these habitats, a methyl-coenzyme M reductase-like enzyme was isolated (Kraăger et al 2003) This protein harbored a nickel- containing prosthetic group that was identified as a heavier (mass of 951 Da) variant of coenzyme F430 (mass of 905 Da), the unique nickel porphinoid in Mcr These studies led to the proposal that anaerobic methane oxidation biochemically, in principle, is a reversal of methanogenesis For more details on anaerobic methane oxidation, see > Chap 17, ‘‘Anaerobic Biodegradation of Hydrocarbons Including Methane’’ in this volume Regulation of Gene Expression Regulation of Catabolic Enzymes by Substrate Availability Many methanoarchaea use only one or two energy substrates so that one may not expect extensive metabolic regulation Nevertheless, it was found that even organisms using H2/CO2 as the sole growth substrate regulate the formation of some key catabolic enzymes in response to the availability of H2 One example is the differential expression of two methyl-coenzyme M reductase isoenzymes in the Methanobacteriales and the Methanococcales (Thauer 1998) In Methanothermobacter species, isoenzyme I is encoded by the mcrBDCGA operon, and isoenzyme II is encoded by the mrtBDGA operon The two isoenzymes differ in their catalytic properties Isoenzyme I has a lower Vmax as compared to isoenzyme II but displays lower KM values for its substrates, CoB-SH and methyl-coenzyme M (Bonacker et al 1993) Expression of the two isoenzymes is differently regulated by the availability of hydrogen Isoenzyme I is predominantly formed when growth is limited by the H2 supply whereas isoenzyme II predominates when the H2 supply is not growth-rate limiting (Bonacker et al 1992; Morgan et al 1997) In the latter case, the methyl-coenzyme M reductase reaction might be a bottleneck of the pathway Therefore, it could be of physiological relevance to synthesize an enzyme with a higher Vmax There are conflicting results with respect to the regulation of other methanogenic enzymes in response to the H2 availability Two groups found that the formation of Hmd in Methanothermobacter species parallels that of isoenzyme II of Mcr (encoded by the mrt operon), while the formation of Frh and Mtd parallels that of isoenzyme I of Mcr (encoded by the mcr operon; Morgan et al 1997; Vermeij et al 1997) Two other groups did not observe a formation of these enzymes in response to H2 availability with their systems (Afting et al 2000; Luo et al 2002) But all groups observed the same pattern of formation of McrI and McrII The formation of flagella in Methanocaldococcus jannaschii is another example of regulation in response to H2 availability Although flagella are not directly involved in catabolic processes, they are essential for finding optimal substrate conditions Under H2-excess conditions, M jannaschii cells are devoid of flagella and have almost undetectable levels of four flagellarelated proteins Flagella synthesis occurs when H2 becomes limiting (Mukhopadhyay et al 2000) Physiology and Biochemistry of the Methane-Producing Archaea Many species of hydrogenotrophic methanogens use formate in place of H2 as the electron donor for CO2 reduction The ability to use formate is attributed to formate dehydrogenase (Fdh), which in methanoarchaea catalyzes the formatedependent reduction of coenzyme F420 The Methanococcus maripaludis genome contains two formate dehydrogenase gene clusters The transcription of both gene clusters was found to be controlled by the availability of H2 Only in the absence of H2 was maximal expression of both fdh gene clusters observed In contrast, formate had no marked effect on the expression (Wood et al 2003) In contrast, expression of formate dehydrogenase in Methanobacterium formicicum seems not to be regulated (Schauer and Ferry 1980) Methanogenium thermophilum can use 2-propanol as sole electron donor for CO2 reduction The secondary alcohol dehydrogenase responsible for 2-propanol oxidation was only formed when H2 became limiting, irrespective of the presence of the alcohol In other methanoarchaea able to grow with secondary alcohols, formation of alcohol dehydrogenase was dependent on the availability of an alcohol, irrespective of the presence of H2 (Widdel and Wolfe 1989) Another response to H2 limitation is the synthesis of an autolytic enzyme by Methanobacterium wolfei (Kiener et al 1987) The physiological role of this suicidal process is not known It may be related to the induction of a defective bacteriophage (Stettler et al 1995) The regulation of the genes encoding methanogenesis from acetate in Methanosarcina species is also well studied Early work had already shown that acetate is only used as energy substrate when none of the higher energy-yielding substrates methanol, methylamines, or H2/CO2 are available, indicating that acetate catabolism is repressed by these other substrates (reviewed in Zinder 1993) This is consistent with the observation that the key enzymes of acetate metabolism (i.e., acetate kinase, phosphotransacetylase, acetyl-CoA synthase/carbon monoxide dehydrogenase complex, and carbonic anhydrase) are formed at a lower level in cells grown on methanol as compared to acetategrown cells (Jablonski et al 1990) Regulation was shown to be at the mRNA level (Sowers et al 1993; Singh-Wissmann and Ferry 1995) On the other hand, most of the enzymes necessary for the reversible reduction of CO2 to the level of methyltetrahydromethanopterin are present at a much lower level in acetate-grown cells (Jablonski et al 1990; Mukhopadhyay et al 1993) When Methanosarcina spp are cultivated on methanol in the presence of H2/CO2, the oxidative branch of the methylotrophic pathway is repressed This result is consistent with the observation that several enzymes of this pathway are formed at a lower level under these conditions (Mukhopadhyay et al 1993) In conclusion, catabolic gene expression in Methanosarcina appears similar to systems in bacteria, which are regulated for preferential utilization of the most energetically favorable substrate For none of the regulatory systems described above has the primary sensor and the signal transduction cascade been elucidated However, in Methanothermobacter thermautotrophicus, studies have been performed which led to the proposal 18 that coenzyme F390 could function as a reporter compound for H2 limitation Coenzyme F390 is formed from coenzyme F420 by adenylation or guanylation at its 8-hydroxy-group This reaction is catalyzed by coenzyme F390 synthetase (Vermeij et al 1994) This enzyme specifically uses oxidized coenzyme F420 as substrate, while reduced coenzyme F420 (F420H2) acts as a competitive inhibitor Coenzyme F390 can be hydrolyzed to coenzyme F420 and AMP or GMP in a reaction catalyzed by coenzyme F390 hydrolase (Vermeij et al 1995) This latter enzyme is redox sensitive and is inactivated by O2 Furthermore, this enzyme is activated by CoM-SH but inactivated by CoM-S-S-CoB On the basis of the biochemical properties of these two enzymes, it has been predicted that the level of coenzyme F390 should be low when cells receive sufficient H2 (which leads to a high coenzyme F420H2 to coenzyme F420 ratio and high CoM-SH to CoM-S-S-CoB ratio) Conversely, the coenzyme F390 concentration in the cell should increase when H2 becomes limiting This prediction was confirmed experimentally (Vermeij et al 1997) In further studies, a Methanothermobacter thermautotrophicus mutant was isolated that was unable to grow under H2-deprived conditions This mutant was also unable to form coenzyme F390 It also lacked the ability to synthesize isoenzyme I of Mcr, which is the enzyme preferentially synthesized under H2-limiting conditions (Pennings et al 1998) This gives further evidence for an important role of coenzyme F390 in the response of the cell to varying H2 concentrations Regulation of Catabolic Enzymes by Trace Element Availability In the methanogenic pathways, enzymes containing transition metals in their active site play an essential role Therefore, not surprisingly, these organisms have developed strategies to cope with limitations on the availability of these metal ions One example is the synthesis of different isoenzymes of formylmethanofuran dehydrogenase (Fmd; reviewed in Vorholt and Thauer 2002) Methanothermobacter marburgensis and Methanothermobacter wolfei form two different isoenzymes, one containing tungsten bound to the molybdopterin cofactor (Fmd-W) and a second containing molybdenum bound to the molybdopterin cofactor (Fmd-M) Whereas Fmd-W is formed constitutively, Fmd-M is only formed when molybdenum is available (Hochheimer et al 1996) A DNA-binding protein, called ‘‘Tfx,’’ was found to specifically bind to a DNA region downstream of the promoter of the fmdECB operon, which encodes Fmd-M Therefore, Tfx may be a transcriptional regulator of the fmdECB operon (Hochheimer et al 1999) A different set of Fmd enzymes is found in Methanopyrus kandleri This organism forms two tungsten-containing Fmd isoenzymes (Vorholt et al 1997) One isoenzyme (called ‘‘Fwu’’) contains selenium, whereas the second (called ‘‘Fwc’’) does not In general, Fmd contains a conserved cysteine residue, which is also conserved in other molybdopterin-containing 655 656 18 Physiology and Biochemistry of the Methane-Producing Archaea enzymes From the crystal structure of other molybdopterincontaining enzymes, for example, dimethylsulfoxide reductase, this residue is known to provide a ligand to the molybdenum center In Fwu, this cysteine residue is replaced by selenocysteine The gene encoding the catalytic subunit FwuB is in the polycistronic operon fwuGDB The gene encoding FwcB, the catalytic subunit of Fwc, is transcribed monocistronically During growth of the organism on medium supplemented with selenium, only the fwuGDB operon is transcribed During growth under selenium limitation, both fwuGDB and fwcB are transcribed Selenium-dependent gene expression has also been observed in Methanococcus voltae In this organism, two isoenzymes of the coenzyme F420-reducing hydrogenase (called ‘‘Fru’’ and ‘‘Frc’’) and two isoenzymes of the coenzyme F420-nonreducing hydrogenase (called ‘‘Vhu’’ and ‘‘Vhc’’) are encoded in the genome (Sorgenfrei et al 1997) One enzyme of each type, Fru and Vhu, contains selenocysteine in the hydrogen-activating reactive site The corresponding isoenzymes, Frc and Vhc, have a cysteinyl residue in the homologous positions The two selenium-containing hydrogenases are constitutively expressed The operons vhc and frc encoding the selenium-free enzymes are only transcribed under selenium limitation They are connected by a common intergenic region comprising both promoters and positive and negative regulatory sequence elements, which were defined by mutational analyses employing a reporter gene system (Noll et al 1999) A putative activator protein has been identified but not yet further characterized (Muăller and Klein 2001) A protein binding to a negative regulatory element involved in the regulation of the two operons was purified Through the identification of the corresponding gene, the protein was found to be a LysR-type regulator It was named ‘‘HrsM’’ (hydrogenase gene regulator, selenium dependent in M voltae) Also, hrsM knockout mutants constitutively transcribed the vhc and frc operons in the presence of selenium (Sun and Klein 2004) Nickel is an essential trace element for methanoarchaea Studies with Methanothermobacter marburgensis have shown that this organism has developed a strategy to spare nickel under nickel limitation As outlined above, coenzyme F420-reducing hydrogenase (Frh), which is a [NiFe] hydrogenase, can be functionally replaced by the combined action of Hmd and Mtd These two latter enzymes not contain Ni When M marburgensis was cultivated under nickel-limited conditions, the specific activity of Hmd and Mtd was six- and fourfold higher and that of Frh up to 180-fold lower than in cells grown on nickel-sufficient medium The frh transcripts were no longer detectable in cells grown under Ni limitation, whereas the relative abundance of the hmd and mtd transcripts increased (Afting et al 1998, 2000) Regulation of Nitrogen Assimilation Nitrogen assimilation by Methanococcus maripaludis is highly regulated This organism fixes N2 but can also use ammonia or alanine as sole nitrogen sources In the presence of ammonia or alanine, N2 fixation is highly repressed (Cohen-Kupiec et al 1997; Lie and Leigh 2002) The repressor has been isolated and is very unusual for this class of proteins Called ‘‘NrpR,’’ it possesses very low sequence similarity to previously described DNA-binding proteins in the prokaryotes (Lie and Leigh 2003) NrpR also regulates the expression of glnA in M maripaludis In addition to transcriptional regulation, N2 fixation is also regulated by a switch-off mechanism Upon the addition of ammonia or alanine, nitrogen fixation ceases immediately (Kessler et al 2001; Lie and Leigh 2002) This regulation requires the participation of two GlnB homologues encoded by nifI1 and nifI2 Although this system acts very similarly to the bacterial system for the posttranslational ADP-ribosylation of the nitrogenase reductase, its mechanism of action is not currently known Bioenergetics of Growth Coupling Sites in Methanogenesis Energy conservation by methanoarchaea is via electron transport phosphorylation as outlined above The H2/CO2 pathway contains two energy-coupling sites: the H4MPT:coenzyme M methyltransferase reaction and the reduction of the heterodisulfide While the methyltransferase reaction is coupled to the primary extrusion of Na+, the heterodisulfide reductase reaction is coupled to the extrusion of H+ Experimental proof that the latter reaction is coupled to energy conservation is, however, only available for Methanosarcina species Via a Na+/H+ antiporter, D:mNa+ and D:mH+ are interconvertible (Kaesler and Schoănheit 1989) Part of the energy conserved in these ion gradients is used to drive the reduction of CO2 to formylmethanofuran by reversed electron transport, while the remaining part of the energy is used for the synthesis of ATP via ATP synthase Methanoarchaea contain A1A0 ATP synthases characteristic for archaea (Moăller 2004) In M thermautotrophicus and Methanosarcina mazei, this is the only ATP synthase encoded in the genome sequences In contrast, the genomes of M barkeri and M acetivorans encode both (an A1A0 ATP synthase and a F1F0 ATP synthase) Expression of the latter enzyme in M barkeri could, however, not be demonstrated (Moăller 2004) The ion specificity of A1A0 ATP synthases is not yet established In silico analysis of the proteolipid of some A1A0 ATP synthases reveal the presence of a Na+ binding motif and suggest that these enzymes use Na+ as coupling ion (Moăller 2004) In aceticlastic methanogenesis, the methyltransferase and the heterodisulfide reductase reactions are also sites of energy conservation Formation of H2 from reduced ferredoxin, catalyzed by Ech hydrogenase, might represent an additional energy-coupling site (> Fig 18.14) On the other hand, activation of acetate to acetyl-CoA requires at least one ATP in Methanosarcina spp and two ATP in Methanosaeta spp Thus, cells must recover the high cost of acetate activation Physiology and Biochemistry of the Methane-Producing Archaea When methanol or methylamines are used as energy substrates, the heterodisulfide reductase reaction is also a site of energy conservation However, the H4MPT:coenzyme M methyltransferase and the formylmethanofuran dehydrogenase reactions now operate in reverse Thus, the methyltransferase reaction becomes energy consuming while the oxidation of formylmethanofuran to CO2 and methanofuran is coupled to energy conservation Growth Yields Methanoarchaea possess specialized systems to generate the energy needed for growth from the process of methanogenesis, and they have only a limited capacity to metabolize complex carbon compounds Even the secondary alcohols, which can serve as electron donors for CO2 reduction in some species, are only partially oxidized to ketones About half of the described species of methanogens are capable of autotrophic growth and obtain all of their cellular carbon from CO2 While the remainder may require organic compounds for growth, these compounds are assimilated into cellular carbon and not extensively metabolized Compounds typically assimilated include acetate and the volatile fatty acids like isovalerate, 2-methylbutyrate, isobutyrate, and propionate, which are common in anaerobic environments, as well as amino acids The inability to assimilate complex organic compounds has profound effects on the energy requirements for growth On the basis of biosynthetic pathways known and inferred from the genomic sequence, Methanococcus maripaludis, a typical hydrogenotrophic methanogen, must expend 89 mmol of ATP equivalents and 97 mmol of [2H] for the biosynthesis of a gram of cells from CO2 (> Table 18.4) Given that 50 % of the cell is carbon, the amount of reductant required is close to 84 mmol of Table 18.4 Bioenergetic requirements for monomer biosynthesis during growth of methanogens in mineral and rich media Requirement (mmol/g of cell dry wt.) a Growth conditions $Pa [2H]b Total [2H]c Autotrophic growth in mineral medium + acetate 89 97 451 89 34 388 Rich mediumd 63 25 276 E coli minimal medium 21 18 – ATP equivalents required Reductant as NADH or H2 equivalents required for anabolism c Includes the H2 necessary for methanogenesis to make ATP with a stoichiometry of ATP/CH4 d Includes acetate + the volatile fatty acids for branched-chain amino acid biosynthesis + aryl acids for aromatic amino acid biosynthesis + the nucleobases (guanine, adenine, and uracil) commonly taken up by the salvage pathway b 18 [2H], or the theoretical amount necessary to reduce 42 mmol of CO2 to the oxidation state of carbon in the cell Presumably, the difference is due to oxidations that occur during biosynthesis and the approximation of the cell composition The ATP requirement greatly exceeds that of a typical heterotroph such as E coli growing in a minimal medium It is also much larger than the approximately 36 mmol ATP (gram of cells)À1 required for polymerization reactions, which includes protein, DNA and RNA biosynthesis (Forrest and Walker 1971; Ingraham et al 1983) Thus, monomer biosynthesis is the major energy demand for growth of a hydrogenotrophic methanogen, and the assimilation of organic carbon sources may have large effects on their growth Many methanogens assimilate exogenous acetate, which is frequently abundant in anaerobic habitats From the biosynthetic pathways, about 16 mmol of acetyl-CoA are utilized in the biosynthesis of one gram of cells; hence, acetate has the potential of providing about 75 % of the cellular carbon Assuming that two ATPs are consumed to active acetate via the high affinity acetyl-CoA synthetase reaction, there is no savings in the ATP requirement for growth when compared with CO2 fixation (> Table 18.4) If only one ATP is utilized to activate acetate via the low affinity acetate kinase reaction, about 16 mmol of ATP is spared, which is about 18 % of the total ATP requirement for monomer biosynthesis Similarly, methanogens frequently assimilate the branched-chain volatile fatty acids as sources of branched-chain amino acids and aryl acids as a source of aromatic amino acids Together, these amino acids account for about 25 % of the cellular carbon Assuming that the carboxylic acids are assimilated by an acyl-CoA synthetase reaction requiring two ATP equivalents, followed by ferredoxindependent oxidoreductase requiring one ATP equivalent to activate the reductant and one [2H], and an aminotransferase (which requires one ATP and one [2H] to make glutamate), four ATP equivalents and two [2H] are required for each amino acid biosynthesized Even then, this pathway results in a large reduction in the energy requirements for growth (> Table 18.4) The maximum cell yields can be estimated For a hydrogenotrophic methanogen fixing CO2 as its major carbon source, about 89 and 36 mmol of ATP per gram of cells are required for monomer biosynthesis and polymerization reactions, respectively Thus, the maximal cell yield is expected to be about 8.0 g of cell dry weight per mol of ATP For a hydrogenotrophic methanogen obtaining carbon from acetate, the volatile fatty acids and aryl acids, the yield is about 10 g of cell dry weight per mol of ATP In contrast, for a heterotroph, the maximal cell yield is 28 g of cell dry weight per mol of ATP For an autotroph using the Calvin cycle of CO2 fixation, the maximal cell yield is 4.75 g of cell dry weight per mol of ATP (Forrest and Walker 1971) Thus, while the cell yield of an autotrophic methanogen is considerably less than that of a heterotroph, it theoretically could be nearly twice that of a chemolithotroph using the Calvin cycle For comparison, the observed cell yield for methanogens are usually in the range of 1–6 g of cells per mol of methane, and the measured maximal cell yields are 3–6 g of cells per mol of 657 658 18 Physiology and Biochemistry of the Methane-Producing Archaea Table 18.5 Genomic sequences of methanoarchaea Genome size (kbp) Number of ORFs Comments Reference(s) Methanothermobacter thermautotrophicus )H 1,751 1,855 Thermophilic hydrogenotroph Smith et al (1997) Methanocaldococcus jannaschii JAL-1 1,723 1,726 Hyperthermophilic hydrogenotroph Bult et al (1996) Methanococcoides burtonii 2,668 2,676 Partial sequence, psychrotolerant methylotroph Saunders et al (2003) Methanococcus maripaludis S2 1,661 1,722 Mesophilic hydrogenotroph Hendrickson et al (2004) Methanogenium frigidum 1,598 1,815 Partial sequence, psychrophilic hydrogenotroph Saunders et al (2003) Methanopyrus kandleri AV19 1,695 1,692 Hyperthermophilic hydrogenotroph Slesarev et al (2002) Methanosarcina acetivorans C2A 5,751 4,524 Mesophilic acetotroph and methylotroph Galagan et al (2002) Methanosarcina barkeri Fusaro 4,830 5,066 Partial, mesophilic acetotroph and methylotroph Joint Genome Institute, unpublished Methanosarcina mazei Goă1 4,096 3,371 Mesophilic acetotroph and methylotroph Deppenmeier et al (2002) Organism methane (Vogels et al 1988; Tsao et al 1994; Schill et al 1996) In the literature, the Methanosarcina species appear to have higher growth yields on H2/CO2 than Methanothermobacter species and others, but these results are from different laboratories and observed under different growth conditions Following cultivation of two mesophiles, Methanosarcina barkeri and Methanobrevibacter aboriphilus, under the similar conditions on H2/CO2, the cell yields were 4.2 g and 1.4 g of dry cells per mol of CH4, respectively (R Hedderich, unpublished data) These results confirmed the lower cell yield among the Methanobacteriales Possibly, the lower cell yield might result from a different mechanism of coupling methanogenesis to the proton motive force or from higher maintenance energy during growth Genomes of the Methanoarchaea The complete genomes have been sequenced in a representative of every order of the methanoarchaea except the Methanomicrobiales, where only a partial sequence is available (> Table 18.5) The sizes of the genomes vary from 1.6 to 5.8 Mbp, reflecting the great diversity in this group of organisms (> Table 18.5) In general, the genomes of the hydrogenotrophic methanogens are smaller, in the range of 1.6–1.8 Mbp Even among these small genomes, the gene content is not highly conserved, and only about two-thirds of the genes in any one organism are likely to be conserved within the methanoarchaea (W B Whitman, unpublished observation) The genomes of the methylotrophic methanogens are much larger, in the range of 2.7–5.8 Mbp In the Methanosarcina spp., the large genome seems to have followed the acquisition of a large number of genes from the anaerobic Firmicutes (Deppenmeier et al 2002) and may be responsible in part for the wide substrate specificity of these organisms (Galagan et al 2002) The growth temperature optima of those methanoarchaea whose genomic sequences have been determined are 15–98 C Thus, it has been possible to make detailed correlations of certain structural features in proteins and nucleic acids with growth temperature (Saunders et al 2003) The amino acid leucine was highly enriched in the proteins from organisms with high growth temperatures, while the amino acids glutamine and threonine were highly enriched at low growth temperatures In addition, the proteins of organisms with high growth temperatures were enriched in the mean fraction of charged residues in the solvent accessible as well as solvent inaccessible areas Likewise, the contribution of hydrophobic residues to the solvent accessible area decreased with growth temperature The tRNAs of organisms with high growth temperatures also possessed higher mol% G + C contents, especially in the stem regions (Saunders et al 2003) References Abbanat DR, Ferry JG (1991) Resolution of component proteins in an enzyme complex from Methanosarcina thermophila catalyzing the synthesis or cleavage of acetyl-CoA Proc Natl Acad Sci USA 88:3272–3276 Abken HJ, Tietze M, Brodersen J, Baăumer S, Beifuss U, Deppenmeier U (1998) Isolation and characterization of methanophenazine and function of phenazines in membrane-bound electron transport of Methanosarcina mazei Goă1 J Bacteriol 180:20272032 Physiology and Biochemistry of the Methane-Producing Archaea Afting C, Hochheimer A, Thauer RK (1998) Function of H2-forming methylenetetrahydromethanopterin dehydrogenase from Methanobacterium thermoautotrophicum in coenzyme F420 reduction with H2 Arch Microbiol 169:206–210 Afting C, Kremmer E, Brucker C, Hochheimer A, Thauer RK (2000) Regulation of the synthesis of H2-forming methylenetetrahydromethanopterin dehydrogenase (Hmd) and of HmdII and HmdIII in Methanothermobacter marburgensis Arch Microbiol 174:225–232 Allen JR, Clark DD, Krum JG, Ensign SA (1999) A role for coenzyme M (2mercaptoethanesulfonic acid) in a bacterial pathway of aliphatic epoxide carboxylation Proc Natl Acad Sci USA 96:8432–8437 Banerjee RV, Johnston NL, Sobeski JK, Datta P, Matthews RG (1989) Cloning and sequence analysis of the Escherichia coli metH gene encoding cobalamindependent methionine synthase and isolation of a tryptic fragment containing the cobalamin-binding domain J Biol Chem 264:13888–13895 Baughn AD, Malamy MH (2004) The strict anaerobe Bacteroides fragilis grows in and benefits from nanomolar concentrations of oxygen Nature 427:441444 Baăumer S, Ide T, Jacobi C, Johann A, Gottschalk G, Deppenmeier U (2000) The F420H2 dehydrogenase from Methanosarcina mazei is a redox-driven proton pump closely related to NADH dehydrogenases J Biol Chem 275:17968– 17973 Bonacker LG, Baudner S, Thauer RK (1992) Differential expression of the two methyl-coenzyme M reductases in Methanobacterium thermoautotrophicum as determined immunochemically via isoenzyme-specific antisera Eur J Biochem 206:8792 Bonacker LG, Baudner S, Moărschel E, Boăcher R, Thauer RK (1993) Properties of the two isoenzymes of methyl-coenzyme M reductase in Methanobacterium thermoautotrophicum Eur J Biochem 217:587–595 Boone DR (2001) Class I: Methanobacteria In: Boone DR, Castenholtz RW, Garrity GM (eds) Bergey’s manual of systematic bacteriology, vol 1, 2nd edn Springer, New York, p 213 Boone DR, Whitman WB, Rouvie`re P (1993) Diversity and taxonomy of methanogens In: Ferry JG (ed) Methanogenesis Chapman & Hall, New York, pp 3580 Bruăggemann H, Falinski F, Deppenmeier U (2000) Structure of the F420H2: quinone oxidoreductase of Archaeoglobus fulgidus identification and overproduction of the F420H2-oxidizing subunit Eur J Biochem 267: 5810–5814 Bult CJ, White O, Olsen GJ, Zhou L, Fleischmann RD, Sutton GG, Blake JA, FitzGerald LM, Clayton RA, Gocayne JD, Kerlavage AR, Dougherty BA, Tomb J-F, Adams MD, Reich CI, Overbeek R, Kirkness EF, Weinstock KG, Merrick JM, Glodek A, Scott JL, Geoghagen NSM, Weidman JF, Fuhrmann JL, Nguyen D, Utterback TR, Kelley JM, Peterson JD, Sadow PW, Hanna MC, Cotton MD, Roberts KM, Hurst MA, Kaine BP, Borodovsky M, Klenk H-P, Fraser CM, Smith HO, Woese CR, Venter JC (1996) Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii Science 273:1058–1073 Buurman G, Shima S, Thauer RK (2000) The metal-free hydrogenase from methanogenic archaea: evidence for a bound cofactor FEBS Lett 485:200–204 Chistoserdova L, Vorholt JA, Thauer RK, Lidstrom ME (1998) C1 transfer enzymes and coenzymes linking methylotrophic bacteria and methanogenic archaea Science 281:99–102 Choi KP, Bair TB, Bae YM, Daniels L (2001) Use of transposon Tn5367 mutagenesis and a nitroimidazopyran-based selection system to demonstrate a requirement for fbiA and fbiB in coenzyme F420 biosynthesis by Mycobacterium bovis BCG J Bacteriol 183:7058–7066 Cohen-Kupiec R, Blank C, Leigh JA (1997) Transcriptional regulation in archaea: in vivo demonstration of a repressor binding site in a methanogen Proc Natl Acad Sci USA 94:1316–1320 Conrad R (1996) Soil microorganisms as controllers of atmospheric trace gases (H2, CO, CH4, OCS, N2O, and NO) Microbiol Rev 60:609–640 Dai YR, Reed DW, Millstein JH, Hartzell PL, Grahame DA, DeMoll E (1998) Acetyl-CoA decarbonylase/synthase complex from Archaeoglobus fulgidus Arch Microbiol 169:525–529 Darnault C, Volbeda A, Kim EJ, Legrand P, Vernede X, Lindahl PA, FontecillaCamps JC (2003) Ni-Zn-[Fe4-S4] and Ni-Ni-[Fe4-S4] clusters in closed and 18 open subunits of acetyl-CoA synthase/carbon monoxide dehydrogenase Nat Struct Biol 10:271–279 Deppenmeier U (1995) Different structure and expression of the operons encoding the membrane-bound hydrogenases from Methanosarcina mazei Goă1 Arch Microbiol 164:370376 Deppenmeier U (2002) The unique biochemistry of methanogenesis Progr Nucl Acid Res Mol Biol 71:223–283 Deppenmeier U (2004) The membrane-bound electron transport system of Methanosarcina species J Bioenerg Biomembr 36:55–64 Deppenmeier U, Blaut M, Lentes S, Herzberg C, Gottschalk G (1995) Analysis of the vhoGAC and vhtGAC operons from Methanosarcina mazei strain Goă1, both encoding a membrane-bound hydrogenase and a cytochrome b Eur J Biochem 227:261269 Deppenmeier U, Muăller V, Gottschalk G (1996) Pathways of energy conservation in methanogenic archaea Arch Microbiol 165:149–163 Deppenmeier U, Lienard T, Gottschalk G (1999) Novel reactions involved in energy conservation by methanogenic archaea FEBS Lett 457:291–297 Deppenmeier U, Johann A, Hartsch T, Merkl R, Schmitz RA, Martinez-Arias R, Henne A, Wiezer A, Baăumer S, Jacobi C, Bruăggemann H, Lienard T, Christmann A, Boămeke M, Steckel S, Bhattacharyya A, Lykidis A, Overbeek R, Klenk H-P, Gunsalus RP, Fritz H-J, Gottschalk G (2002) The genome of Methanosarcina mazei: evidence for lateral gene transfer between bacteria and Archaea J Mol Microbiol Biotechnol 4:453–461 Dighe AS, Jangid K, Gonza´lez JM, Pidiyar VJ, Patole MS, Ranade DR, Shouche YS (2004) Comparison of 16S rRNA gene sequences of genus Methanobrevibacter BMC Microbiol 4(20) DiMarco AA, Bobik TA, Wolfe RS (1990) Unusual coenzymes of methanogenesis Annu Rev Biochem 59:355–394 Dobbek H, Svetlitchnyi V, Gremer L, Huber R, Meyer O (2001) Crystal structure of a carbon monoxide dehydrogenase reveals a [Ni-4Fe-5S] cluster Science 293:1281–1285 Drennan CL, Heo J, Sintchak MD, Schreiter E, Ludden PW (2001) Life on carbon monoxide: X-ray structure of Rhodospirillum rubrum Ni-Fe-S carbon monoxide dehydrogenase Proc Natl Acad Sci USA 98:11973–11978 Duin EC, Bauer C, Jaun B, Hedderich R (2003) Coenzyme M binds to a [4Fe-4S] cluster in the active site of heterodisulfide reductase as deduced from EPR studies with the [33S]coenzyme M-treated enzyme FEBS Lett 538:81–84 Ensign SA, Allen JR (2003) Aliphatic epoxide carboxylation Annu Rev Biochem 72:55–76 Ermler U, Grabarse W, Shima S, Goubeaud M, Thauer RK (1997) Crystal structure of methyl-coenzyme M reductase: the key enzyme of biological methane formation Science 278:1457–1462 Ferguson DJ Jr, Gorlatova N, Grahame DA, Krzycki JA (2000) Reconstitution of dimethylamine:coenzyme M methyl transfer with a discrete corrinoid protein and two methyltransferases purified from Methanosarcina barkeri J Biol Chem 275:29053–29060 Ferry JG (1997) Enzymology of the fermentation of acetate to methane by Methanosarcina thermophila Biofactors 6:25–35 Ferry JG (1999) Enzymology of one-carbon metabolism in methanogenic pathways FEMS Microbiol Rev 23:13–38 Forrest WW, Walker DJ (1971) The generation and utilization of energy during growth Adv Microbiol Physiol 5:213–274 Franzmann PD, Springer N, Ludwig W, Conway de Macario E, Rohde M (1992) A methanogenic archaeon from Ace Lake, Antarctica: Methanococcoides burtonii sp nov Syst Appl Microbiol 15:573–581 Franzmann PD, Liu Y, Balkwill DL, Aldrich HC, Conway de Macario E, Boone DR (1997) Methanogenium frigidum sp nov., a psychrophilic, H2-using methanogen from Ace Lake, Antartica Int J Syst Bacteriol 47:1068–1072 Galagan JE, Nusbaum C, Roy A, Endrizzi MG, Macdonald P, FitzHugh W, Calvo S, Engels R, Smirnov S, Atnoor D, Brown A, Allen N, Naylor J, Stange-Thomann N, DeArellano K, Johnson R, Linton L, McEwan P, McKernan K, Talamas J, Tirrell A, Ye W, Zimmer A, Barber RD, Cann I, Graham DE, Grahame DA, Guss AM, Hedderich R, Ingram-Smith C, Kuettner HC, Krzycki JA, Leigh JA, Li W, Liu J, Mukhopadhyay B, Reeve JN, Smith K, Springer TA, Umayam LA, White O, White RH, Conway de Macario E, Ferry JG, Jarrell KF, Jing H, Macario AJ, Paulsen I, Pritchett M, 659 660 18 Physiology and Biochemistry of the Methane-Producing Archaea Sowers KR, Swanson RV, Zinder SH, Lander E, Metcalf WW, Birren B (2002) The genome of M acetivorans reveals extensive metabolic and physiological diversity Genome Res 12:532542 Gaărtner P, Ecker A, Fischer R, Linder D, Fuchs G, Thauer RK (1993) Purification and properties of N5-methyltetrahydromethanopterin:coenzyme M methyltransferase from Methanobacterium thermoautotrophicum Eur J Biochem 213:537–545 Gencic S, Grahame DA (2003) Nickel in subunit beta of the acetyl-CoA decarbonylase/synthase multienzyme complex in methanogens Catalytic properties and evidence for a binuclear Ni-Ni site J Biol Chem 278:6101– 6110 Goenrich M, Mahlert F, Duin EC, Bauer C, Jaun B, Thauer RK (2004) Probing the reactivity of Ni in the active site of methyl-coenzyme M reductase with substrate analogues J Biol Inorg Chem 9:691–705 Gorris LG, van der Drift C (1994) Cofactor contents of methanogenic bacteria reviewed Biofactors 4:139–145 Gorris LG, Voet AC, van der Drift C (1991) Structural characteristics of methanogenic cofactors in the non-methanogenic archaebacterium Archaeoglobus fulgidus Biofactors 3:29–35 Gottschalk G, Thauer RK (2001) The Na+-translocating methyltransferase complex from methanogenic archaea Biochim Biophys Acta 1505:28–36 Grahame DA, DeMoll E (1996) Partial reactions catalyzed by protein components of the acetyl-CoA decarbonylase synthase enzyme complex from Methanosarcina barkeri J Biol Chem 271:8352–8358 Hagemeier CH, Shima S, Thauer RK, Bourenkov G, Bartunik HD, Ermler U (2003) Coenzyme F420-dependent methylenetetrahydromethanopterin dehydrogenase (Mtd) from Methanopyrus kandleri: a methanogenic enzyme with an unusual quaternary structure J Mol Biol 332:1047–1057 Hallam SJ, Girguis PR, Preston CM, Richardson PM, DeLong EF (2003) Identification of methyl coenzyme M reductase A (mcrA) genes associated with methane-oxidizing archaea Appl Environ Microbiol 69:5483–5491 Hao B, Gong W, Ferguson TK, James CM, Krzycki JA, Chan MK (2002) A new UAG-encoded residue in the structure of a methanogen methyltransferase Science 296:1462–1466 Harms U, Thauer RK (1997) Identification of the active site histidine in the corrinoid protein MtrA of the energy-conserving methyltransferase complex from Methanobacterium thermoautotrophicum Eur J Biochem 250:783–788 Hedderich R (2004) Energy-converting [NiFe] hydrogenases from archaea and extremophiles: ancestors of complex I J Bioenerg Biomembr 36:6575 Hedderich R, Klimmek O, Kroăger A, Dirmeier R, Keller M, Stetter KO (1998) Anaerobic respiration with elemental sulfur and with disulfides FEMS Microbiol Rev 22:353–381 Hendrickson EL, Kaul R, Zhou Y, Bovee D, Chapman P, Chung J, Conway de Macario E, Dodsworth JA, Gillett W, Graham DE, Hackett M, Haydock AK, Kang A, Land ML, Levy R, Lie TJ, Major TA, Moore BC, Porat I, Palmeiri A, Rouse G, Saenphimmachak C, Soăll D, van Dien S, Wang T, Whitman WB, Xia Q, Zhang Y, Larimer FW, Olson MV, Leigh JA (2004) Complete genome sequence of the genetically tractable hydrogenotrophic methanogen Methanococcus maripaludis J Bacteriol 186:6956–6969 Hippler B, Thauer RK (1999) The energy conserving methyltetrahydromethanopterin:coenzyme M methyltransferase complex from methanogenic archaea: function of the subunit MtrH FEBS Lett 449:165–168 Hochheimer A, Linder D, Thauer RK, Hedderich R (1996) The molybdenum formylmethanofuran dehydrogenase operon and the tungsten formylmethanofuran dehydrogenase operon from Methanobacterium thermoautotrophicum: structures and transcriptional regulation Eur J Biochem 242:156–162 Hochheimer A, Hedderich R, Thauer RK (1999) The DNA binding protein Tfx from Methanobacterium thermoautotrophicum: structure, DNA binding properties and transcriptional regulation Mol Microbiol 31:641–650 Ide T, Baăumer S, Deppenmeier U (1999) Energy conservation by the H2: heterodisulfide oxidoreductase from Methanosarcina mazei Goă1: identification of two proton-translocating segments J Bacteriol 181:4076–4080 Ingraham JL, Maaløe O, Neidhardt FC (1983) Growth of the bacterial cell Sineaur, Sunderland, pp 87–173 Jablonski PE, DiMarco AA, Bobik TA, Cabell MC, Ferry JG (1990) Protein content and enzyme activities in methanol-and acetate-grown Methanosarcina thermophila J Bacteriol 172:1271–1275 James CM, Ferguson TK, Leykam JF, Krzycki JA (2001) The amber codon in the gene encoding the monomethylamine methyltransferase isolated from Methanosarcina barkeri is translated as a sense codon J Biol Chem 276:34252–34258 Jones WJ, Leigh JA, Mayer F, Woese CR, Wolfe RS (1983) Methanococcus jannaschii sp nov., an extremely thermophilic methanogen from a submarine hydrothermal vent Arch Microbiol 136:254261 Kaesler B, Schoănheit P (1989) The sodium cycle in methanogenesis CO2 reduction to the formaldehyde level in methanogenic bacteria is driven by a primary electrochemical potential of Na+ generated by formaldehyde reduction to CH4 Eur J Biochem 186:309316 Kaănkel A, Vorholt JA, Thauer RK, Hedderich R (1998) An Escherichia coli hydrogenase-3-type hydrogenase in methanogenic archaea Eur J Biochem 252:467–476 Kessler PS, Daniel C, Leigh JA (2001) Ammonia switch-off of nitrogen fixation in the methanogenic archaeon Methanococcus maripaludis: mechanistic features and requirement for the novel GlnB homologues, NifI1 and NifI2 J Bacteriol 183:882–889 Keswani J, Whitman WB (2001) Relationship of 16S rRNA sequence similarity to DNA hybridization in prokaryotes Int J Syst Evol Microbiol 51:667–678 Kiener A, Konig H, Winter J, Leisinger T (1987) Purification and use of Methanobacterium wolfei pseudomurein endopeptidase for lysis of Methanobacterium thermoautotrophicum J Bacteriol 169:1010–1016 Klenk HP, Clayton RA, Tomb JF, White O, Nelson KE, Ketchum KA, Dodson RJ, Gwinn M, Hickey EK, Peterson JD, Richardson DL, Kerlavage AR, Graham DE, Kyrpides NC, Fleischmann RD, Quackenbush J, Lee NH, Sutton GG, Gill S, Kirkness EF, Dougherty BA, McKenney K, Adams MD, Loftus B, Peterson S, Reich CI, McNeil LK, Badger JH, Glodek A, Zhou L, Overbeek R, Gocayne JD, Weidmann JF, McDonald L, Utterback T, Cotton MD, Spriggs T, Atriach P, Kaine BP, Sykes SM, Sadow PW, D’Andrea KP, Bowman C, Fujii C, Garland SA, Mason TM, Olsen GJ, Fraser CM, Smith HO, Woese CR, Venter JC (1997) The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus Nature 390:364370 Kraăger M, Meyerdierks A, Glockner FO, Amann R, Widdel F, Kube M, Reinhardt R, Kahnt J, Boăcher R, Thauer RK, Shima S (2003) A conspicuous nickel protein in microbial mats that oxidize methane anaerobically Nature 426:878881 Kraăutler B (1998) B12-coenzymes: the central theme In: Kraăutler B, Arigoni D, Golding B (eds) Vitamin B12 and B12-proteins Wiley, New York, pp 4–43 Kunow J, Linder D, Stetter KO, Thauer RK (1994) F420H2:quinone oxidoreductase from Archaeoglobus fulgidus Characterization of a membrane-bound multisubunit complex containing FAD and iron-sulfur clusters Eur J Biochem 223:503–511 Kurr M, Huber R, Koănig H, Jannasch HW, Fricke H, Trincone A, Kristjansson JK, Stetter KO (1991) Methanopyrus kandleri, gen and sp nov represents a novel group of hyperthermophilic methanogens, growing at 110 C Arch Microbiol 156:239–247 Lie TJ, Leigh JA (2002) Regulatory response of Methanococcus maripaludis to alanine, an intermediate nitrogen source J Bacteriol 184:5301–5306 Lie TJ, Leigh JA (2003) Novel repressor of nif and glnA expression in the methanogenic archaeon Methanococcus maripaludis Mol Microbiol 47:235–246 Lienard T, Becher B, Marschall M, Bowien S, Gottschalk G (1996) Sodium ion translocation by N5-methyltetrahydromethanopterin: coenzyme M methyltransferase from Methanosarcina mazei Goă1 reconstituted in ether lipid liposomes Eur J Biochem 239:857–864 Lomans BP, Maas R, Luderer R, Op den Camp HJM, Pol A, van der Drift C, Vogels GD (1999) Isolation and characterization of Methanomethylovorans hollandica gen nov., sp nov., isolated from freshwater sediment, a methylotrophic methanogen able to grow on dimethyl sulfide and methanethiol Appl Environ Microbiol 65:3641–3650 Physiology and Biochemistry of the Methane-Producing Archaea Luo HW, Zhang H, Suzuki T, Hattori S, Kamagata Y (2002) Differential expression of methanogenesis genes of Methanothermobacter thermoautotrophicus (formerly Methanobacterium thermoautotrophicum) in pure culture and in cocultures with fatty acid-oxidizing syntrophs Appl Environ Microbiol 68:1173–1179 Lyon EJ, Shima S, Boecher R, Thauer RK, Grevels FW, Bill E, Roseboom W, Albracht SP (2004a) Carbon monoxide as an intrinsic ligand to iron in the active site of the iron-sulfur-cluster-free hydrogenase H2-forming methylenetetrahydromethanopterin dehydrogenase as revealed by infrared spectroscopy J Am Chem Soc 126:14239–14248 Lyon EJ, Shima S, Buurman G, Chowdhuri S, Batschauer A, Steinbach K, Thauer RK (2004b) UV-A/blue-light inactivation of the ‘‘metal-free’’ hydrogenase (Hmd) from methanogenic archaea Eur J Biochem 271:195–204 Madadi-Kahkesh S, Duin EC, Heim S, Albracht SPJ, Johnson MK, Hedderich R (2001) A paramagnetic species with unique EPR characteristics in the active site of heterodisulfide reductase from methanogenic archaea Eur J Biochem 268:2566–2577 Maden BE (2000) Tetrahydrofolate and tetrahydromethanopterin compared: functionally distinct carriers in C1 metabolism Biochem J 350(Pt 3):609–629 Mander GJ, Duin EC, Linder D, Stetter KO, Hedderich R (2002) Purification and characterization of a membrane-bound enzyme complex from the sulfatereducing archaeon Archaeoglobus fulgidus related to heterodisulfide reductase from methanogenic archaea Eur J Biochem 269:1895–1904 Meuer J, Bartoschek S, Koch J, Kuănkel A, Hedderich R (1999) Purification and catalytic properties of Ech hydrogenase from Methanosarcina barkeri Eur J Biochem 265:325–335 Meuer J, Kuettner HC, Zhang JK, Hedderich R, Metcalf WW (2002) Genetic analysis of the archaeon Methanosarcina barkeri Fusaro reveals a central role for Ech hydrogenase and ferredoxin in methanogenesis and carbon fixation Proc Natl Acad Sci USA 99:5632–5637 Miller TL (1991) Biogenic sources of methane In: Rogers JE, Whitman WB (eds) Microbial production and consumption of greenhouse gases American Society for Microbiology, Washington, DC, pp 175–187 Miller TL (2001) Genus II: Methanobrevibacter In: Boone DR, Castenholtz RW, Garrity GM (eds) Bergey’s manual of systematic bacteriology, vol 1, 2nd edn Springer, New York, pp 218–226 Miller TL, Lin C (2002) Description of Methanobrevibacter gottschalkii sp nov., Methanobrevibacter thaueri sp nov., Methanobrevibacter woesei sp nov and Methanobrevibacter wolinii sp nov Int J Syst Evol Microbiol 52:819–922 Miller TL, Wolin MJ (1982) Enumeration of Methanobrevibacter smithii in human feces Arch Microbiol 131:1418 Moăller V (2004) An exceptional variability in the motor of archael A1A0 ATPases: from multimeric to monomeric rotors comprising 6–13 ion binding sites J Bioenerg Biomembr 36:115125 Moăller-Zinkhan D, Boărner G, Thauer RK (1989) Function of methanofuran, tetrahydromethanopterin, and coenzyme F420 in Archaeoglobus fulgidus Arch Microbiol 152:362–368 Monson RK, Holland EA (2001) Biospheric trace gas fluxes and their control over tropospheric chemistry Annu Rev Ecol Syst 32:547–576 Morgan RM, Pihl TD, Nolling J, Reeve JN (1997) Hydrogen regulation of growth, growth yields, and methane gene transcription in Methanobacterium thermoautotrophicum &D H J Bacteriol 179:889–898 Mukhopadhyay B, Purwantini E, Daniels L (1993) Effect of methanogenic substrates on coenzyme F420-dependent N5, N10-methylene-H4MPT dehydrogenase, N5, N10-methenyl-H4MPT cyclohydrolase and F420-reducing hydrogenase activities in Methanosarcina barkeri Arch Microbiol 159:141–146 Mukhopadhyay B, Johnson EF, Wolfe RS (2000) A novel pH2 control on the expression of flagella in the hyperthermophilic strictly hydrogenotrophic methanarchaeaon Methanococcus jannaschii Proc Natl Acad Sci USA 97:1152211527 Muăller S, Klein A (2001) Coordinate positive regulation of genes encoding [NiFe] hydrogenases in Methanococcus voltae Mol Genet Genomics 265:1069–1075 Noll I, Muăller S, Klein A (1999) Transcriptional regulation of genes encoding the selenium-free [NiFe]-hydrogenases in the archaeon Methanococcus 18 voltae involves positive and negative control elements Genetics 152:1335–1341 Pennings JL, Keltjens JT, Vogels GD (1998) Isolation and characterization of Methanobacterium thermoautotrophicum DeltaH mutants unable to grow under hydrogen-deprived conditions J Bacteriol 180:2676–2681 Reeburgh WS, Whalen SC, Alperin MJ (1993) The role of methylotrophy in the global methane budget In: Murrell JC, Kelly DP (eds) Microbial growth on C1 compounds Intercept, Andover, pp 114 Reeburoăgh WS (2003) Global methane biogeochemistry In: Keeling RF (ed) Treatise on geochemistry, volume 4: the atmosphere Elsevier/Pergamon, Oxford, pp 65–89 Sauer K, Thauer RK (1997) Methanol:coenzyme M methyltransferase from Methanosarcina barkeri: zinc dependence and thermodynamics of the methanol:cob(I)alamin methyltransferase reaction Eur J Biochem 249:280–285 Saunders NFW, Thomas T, Curmi PMG, Mattick JS, Kuczek E, Slade R, Davis J, Franzmann PD, Boone D, Rusterholtz K, Feldman R, Gates C, Bench S, Sowers K, Kadner K, Aerts A, Dehal P, Detter C, Glavina T, Lucas S, Richardson P, Larimer F, Hauser L, Land M, Cavicchioli R (2003) Mechanisms of thermal adaptation revealed from the genomes of the antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii Genome Res 13:1580–1588 Schauer NL, Ferry JG (1980) Metabolism of formate in Methanobacterium formicicum J Bacteriol 142:800–807 Schill N, van Gulik WM, Voisard D, von Stockar U (1996) Continuous cultures limited by a gaseous substrate: development of a simple, unstructured mathematical model and experimental verification with Methanobacterium thermoautotrophicum Biotechnol Bioeng 51:645–658 Schlesinger WH (1991) Biogeochemistry: an analysis of global change, 2nd edn Academic, New York Seedorf H, Dreisbach A, Hedderich R, Shima S, Thauer RK (2004) F420H2 oxidase (FprA) from Methanobrevibacter arboriphilus, a coenzyme F420-dependent enzyme involved in O2 detoxification Arch Microbiol 182:126–137 Seravalli J, Xiao Y, Gu W, Cramer SP, Antholine WE, Krymov V, Gerfen GJ, Ragsdale SW (2004) Evidence that NiNi acetyl-CoA synthase is active and that the CuNi enzyme is not Biochemistry 43:3944–3955 Setzke E, Hedderich R, Heiden S, Thauer RK (1994) H2: heterodisulfide oxidoreductase complex from Methanobacterium thermoautotrophicum: composition and properties Eur J Biochem 220:139–148 Shima S, Warkentin E, Thauer RK, Ermler U (2002) Structure and function of enzymes involved in the methanogenic pathway utilizing carbon dioxide and molecular hydrogen J Biosci Bioeng 93:519–530 Shima S, Lyon EJ, Sordel-Klippert M, Kauß M, Kahnt J, Thauer RK, Steinbach K, Xie X, Verdier L, Griesinger C (2004) The cofactor of the iron-sulfur cluster free hydrogenase Hmd: structure of the light-inactivation product Angew Chem Int Ed Engl 43:2547–2551 Singh-Wissmann K, Ferry JG (1995) Transcriptional regulation of the phosphotransacetylase-encoding and acetate kinase-encoding genes (pta and ack) from Methanosarcina thermophila J Bacteriol 177:1699–1702 Slesarev AI, Mezhevaya KV, Makarova KS, Polushin NN, Shcherbinina OV, Shakhova VV, Belova GI, Aravind L, Natale DA, Rogozin IB, Tatusov RL, Wolf YI, Stetter KO, Malykh AG, Koonin EV, Kozyavkin SA (2002) The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens Proc Natl Acad Sci USA 99:4644–4649 Smith DR, Douchette-Stamm LA, Deloughery C, Lee H, Dubois J, Aldredge T, Bashirzadeh R, Blakely D, Cook R, Gilbert K, Harrison D, Hoang L, Keagle P, Lumm W, Pothier B, Qiu D, Spadafora R, Vicaire R, Wang Y, Wierzbowski J, Gibson R, Jiwani N, Caruso A, Bush D, Safer H, Patwell D, Prabhakar S, McDougall S, Shimer G, Goyal A, Pietrokovski S, Church GM, Daniels CJ, Mao J-I, Rice P, Noălling J, Reeve JN (1997) Complete genome sequence of Methanobacterium thermoautotrophicum deltaH: functional analysis and comparative genomics J Bacteriol 179:7135–7155 Sorgenfrei O, Muăller S, Pfeiffer M, Sniezko I, Klein A (1997) The [NiFe] hydrogenases of Methanococcus voltae: genes, enzymes and regulation Arch Microbiol 167:189–195 661 662 18 Physiology and Biochemistry of the Methane-Producing Archaea Sowers KR, Thai TT, Gunsalus RP (1993) Transcriptional regulation of the carbon monoxide dehydrogenase gene (cdhA) in Methanosarcina thermophila J Biol Chem 268:23172–23178 Sprenger WW, van Belzen MC, Rosenberg J, Hackstein JHP, Keltjens JT (2000) Methanomicrococcus blatticola gen nov., sp nov., a methanol-and methylamine-reducing methanogen from the hindgut of the cockroach Periplaneta americana Int J Syst Evol Microbiol 50:1989–1999 Srinivasan G, James CM, Krzycki JA (2002) Pyrrolysine encoded by UAG in Archaea: charging of a UAG-decoding specialized tRNA Science 296:1459–1462 Stackebrandt E, Goebel BM (1994) Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology Int J Syst Bacteriol 44:846–849 Stettler R, Thurner C, Stax D, Meile L, Leisinger T (1995) Evidence for a defective prophage on the chromosome of Methanobacterium wolfei FEMS Microbiol Lett 132:85–89 Stojanowic A, Hedderich R (2004) CO2 reduction to the level of formylmethanofuran in Methanosarcina barkeri is non-energy driven when CO is the electron donor FEMS Microbiol Lett 235:163–167 Stojanowic A, Mander GJ, Duin EC, Hedderich R (2003) Physiological role of the F420-non-reducing hydrogenase (Mvh) from Methanothermobacter marburgensis Arch Microbiol 180:194–203 Sun J, Klein A (2004) A lysR-type regulator is involved in the negative regulation of genes encoding selenium-free hydrogenases in the archaeon Methanococcus voltae Mol Microbiol 52:563–571 Svetlitchnyi V, Dobbek H, Meyer-Klaucke W, Meins T, Thiele B, Romer P, Huber R, Meyer O (2004) A functional Ni-Ni-[4Fe-4S] cluster in the monomeric acetyl-CoA synthase from Carboxydothermus hydrogenoformans Proc Natl Acad Sci USA 101:446–451 Tallant TC, Paul L, Krzycki JA (2001) The MtsA subunit of the methylthiol: coenzyme M methyltransferase of Methanosarcina barkeri catalyses both half-reactions of corrinoid-dependent dimethylsulfide: coenzyme M methyl transfer J Biol Chem 276:4485–4493 Tersteegen A, Hedderich R (1999) Methanobacterium thermoautotrophicum encodes two multi-subunit membrane-bound [NiFe] hydrogenases: transcription of the operons and sequence analysis of the deduced proteins Eur J Biochem 264:930–943 Thauer RK (1998) Biochemistry of methanogenesis: a tribute to Marjory Stephenson Microbiology 144:2377–2406 Thauer RK, Sauer K (1999) The role of corrinoids in methanogenesis In: Banerjee R (ed) Chemistry and biochemistry of B12 Wiley, New York, pp 655–679 Thauer RK, Klein AR, Hartmann GC (1996) Reactions with molecular hydrogen in microorganisms: evidence for a purely organic hydrogenation catalyst Chem Rev 96:3031–3042 Tsao J-H, Kaneshiro SM, Yu S-S, Clark DS (1994) Continuous culture of Methanococcus jannaschii, an extremely thermophilic methanogen Biotechnol Bioeng 43:258–261 Tyler SC (1991) The global methane budget In: Rogers JE, Whitman WB (eds) Microbial production and consumption of greenhouse gases American Society for Microbiology, Washington, DC, pp 7–38 Valentine DL, Reeburgh WS (2000) New perspectives on anaerobic methane oxidation Environ Microbiol 2:477–484 Vermeij P, Detmers FJ, Broers FJ, Keltjens JT, van der Drift C (1994) Purification and characterization of coenzyme F390 synthetase from Methanobacterium thermoautotrophicum (strain delta H) Eur J Biochem 226:185–191 Vermeij P, Vinke E, Keltjens JT, van der Drift C (1995) Purification and properties of coenzyme F390 hydrolase from Methanobacterium thermoautotrophicum (strain Marburg) Eur J Biochem 234:592–597 Vermeij P, Pennings JL, Maassen SM, Keltjens JT, Vogels GD (1997) Cellular levels of Factor 390 and methanogenic enzymes during growth of Methanobacterium thermoautotrophicum DeltaH J Bacteriol 179:6640–6648 Vignais PM, Billoud B, Meyer J (2001) Classification and phylogeny of hydrogenases FEMS Microbiol Rev 25:455–501 Vogels GD, Keltjens JT, van der Drift C (1988) Biochemistry of methane production In: Zehnder AJB (ed) Biology of anaerobic microorganisms Wiley, New York, pp 707–770 Vorholt JA, Thauer RK (2002) Molybdenum and tungsten enzymes in C1 metabolism Met Ions Biol Syst 39:571–619 Vorholt JA, Vaupel M, Thauer RK (1997) A selenium-dependent and seleniumindependent formylmethanofuran dehydrogenase and their transcriptional regulation in the hyperthermophilic Methanopyrus kandleri Mol Microbiol 23:1033–1042 Warkentin E, Mamat B, Sordel-Klippert M, Wicke M, Thauer RK, Iwata M, Iwata S, Ermler U, Shima S (2001) Structures of F420H2:NADP+ oxidoreductase with and without its substrates bound EMBO J 20:6561–6569 Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE, Stackebrandt E, Starr MP, Truăper HG (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematics Int J Syst Bacteriol 37:463–464 Weiss DS, Gartner P, Thauer RK (1994) The energetics and sodium-ion dependence of N5-methyltetrahydromethanopterin:coenzyme M methyltransferase studied with cob(I)alamin as methyl acceptor and methylcob(III)alamin as methyl donor Eur J Biochem 226:799–809 Whitman WB, Boone DR, Koga Y, Keswani J (2001) Taxonomy of methanogenic archaea In: Boone DR, Castenholtz RW, Garrity GM (eds) Bergey’s manual of systematic bacteriology, vol 1, 2nd edn Springer, New York, pp 211–213 Widdel F, Wolfe R (1989) Expression of secondary alcohol dehydrogenases in methanogenic bacteria and purification of the F420-specific enzyme from Methanogenium thermophilum strain TCI Arch Microbiol 152:322–328 Wolfe RS (1991) My kind of biology Annu Rev Biochem 45:1–35 Wood GE, Haydock AK, Leigh JA (2003) Function and regulation of the formate dehydrogenase genes of the methanogenic archaeon Methanococcus maripaludis J Bacteriol 185:2548–2554 Wright A-DG, Williams AJ, Winder B, Christophersen CT, Rodgers SL, Smith KD (2004) Molecular diversity of rumen methanogens from sheep in western Australia Appl Environ Microbiol 70:1263–1270 Zhilina TN, Zavarzin GA (1987) Methanohalobium evestigatus, gen nov sp nov., the extremely halophilic methanogenic archaebacterium Dokl Akad Nauk SSSR 293:464–468 Zinder SH (1993) Physiological ecology of methanogens In: Ferry JG (ed) Methanogenesis Chapman & Hall, New York, pp 128–206 ... International Scholar of the NIH, the Pan Lab Prize of the Society of Industrial Microbiology, the Proctor & Gamble Prize of the ASM, the Sakov Prize, the Landau Prize, and the Israel Prize for a... genera and they differ in their morphology, cytology, and physiology The most frequently isolated acetogenic species to date are members of the genera Clostridium and Acetobacterium The habitat, the. .. DeLong, Stephen Lory, Erko Stackebrandt and Fabiano Thompson (Eds.) The Prokaryotes Prokaryotic Physiology and Biochemistry Fourth Edition With 220 Figures and 62 Tables Editor-in-Chief Eugene