The Biochemistry ofArchaea (Archaebacteria)

Editors

M. Kates

Department of Biochemistry, University of Ottawa,Ottawa, Ont. KIN 6N5, Canada

D.J. Kushner

Department of Microbiology, University of Toronto,Toronto, Ont. M5S 1A8, Canada

A.T. Matheson

Department of Biochemistry and Microbiology,University of Victoria, Victoria, B. C. V5Z 4H4, Canada

1993ELSEVffiR

Amsterdam • London • New York • Tokyo

Contents

Preface v

Introduction. The archaea: Their history and significanceCarl R. Woese vii

1. Introduction vii2. Microbiology's changing evolutionary perspective xi3. A molecular definition of the three domains xv4. Archaeal phylogenetic relationships xxi5. The new microbiology xxvAcknowledgment xxviiReferences xxvii

List of contributors xxxi

Chapter 1. Central metabolism of the archaeaM.J. Danson 1

1. Introduction 11.1. Central metabolism 11.2. Central metabolism in eukaryotes and eubacteria : 1

2. Hexose catabolism in the archaea 22.1. The modified Entner-Doudoroff pathway of the halophiles 22.2. The non-phosphorylated pathway of the thermophiles 52.3. The glycolytic pathway of the methanogens 72.4. Gluconeogenesis 72.5. The pentose-phosphate pathway 8

3. Pyruvate oxidation to acetyl-CoA in the archaea 83.1. Pyruvate oxidoreductases 83.2. Comparison with the eukaryotic and eubacterial enzymes 93.3. Dihydrolipoamide dehydrogenase 10

4. The citric acid cycle in the archaea 114.1. The oxidative citric acid cycle 114.2. The reductive citric acid cycle 124.3. Partial citric acid cycles 134.4. Other pathways of acetyl-CoA metabolism I 13

5. Amino acid and lipid metabolism in the archaea 14

6. Evolution of central metabolism 156.1. Hexose catabolism 156.2. Pyruvate oxidation to acetyl-CoA 176.3. The citric acid cycle 17

7. Comparative enzymology of central metabolism 187.1. The enzymes as molecular chronometers 187.2. Citrate synthase 19

7.2.1. The comparative enzymology of citrate synthases 197.2.2. Archaebacterial citrate synthases 19

8. Conclusions and perspectives 20Acknowledgements 20Note added in proof 21References 21

Chapter 2. Bioenergetics of extreme halophilesV.P. Skulachev . 25

1. Introduction 252. A general scheme of energy transduction in extreme halophiles 253. Bacteriorhodopsin and halorhodopsin 27

3.1. Transmembrane charge displacement 273.2. Involvement in photoreception 30

4. Respiratory chain 325. Arginine fermentation 336. H+-ATP-synthase 337. Formation of K+/Na+ gradients. A/iH+ buffering 348. Na+, metabolite symports 359. A flagellar motor 3610. Some prospects for future research 37References 37

Chapter 3. Biochemistry of methanogenesisL. Daniels 41

1. Introduction 412. Novel coenzymes 43

2.1. General 432.2. The 5-deazaflavin, F420 452.3. Methanofuran (MF) 472.4. Tetrahydromethanopterin (H4MPT) 482.5. CoenzymeM 502.6. Cobamides - 512.7. F430 512.8. 7-Mercaptoheptanoylthreonine phosphate (HSHTP) 53

3. The pathways and biochemistry of methanogenesis 533.1. Methanogenesis from CO2 53

3.1.1. Reduction of CO2 533.1.2. The RPG effect 573.1.3. Source of electrons 57

3.2. Methanogenesis from methanol 583.2.1. Reduction of methanol 583.2.2. Oxidation of methanol 593.2.3. Electron transfer 603.2.4. Methanogenesis from methylamines 61

3.3. Methanogenesis from acetate 613.3.1. Transport of acetate into the cell 613.3.2. Activation of acetate 613.3.3. Cleavage of acetyl-CoA and CH3-C0M formation 623.3.4. Reduction of CH3-C0M to CH4 653.3.5. Electron transfer 65

4. Enzymes involved in methanogenesis 664.1. General 664.2. Hydrogenase and non-catalytic redox proteins such as ferredoxin and cytochromes 66

4.2.1. The methylviologen-reducing hydrogenase (MVH) 684.2.2. Redox-active proteins: ferredoxin, cytochromes, and others 694.2.3. The F42o-reducing hydrogenase (FRH) 70

4.3. Alcohol dehydrogenase (ADH) 724.4. Formate dehydrogenase 734.5. Formylmethanofuran dehydrogenase 754.6. Formylmethanofuranrtetrahydromethanopterin formyltransferase 784.7. 7V5,./V10-methenyltetrahydromethanopterin cyclohydrolase 794.8. Methylenetetrahydromethanopterin dehydrogenase 824.9. Methylenetetrahydromethanopterin reductase 854.10. Methyltetrahydromethanopterin:CoM methyltransferase 874.11. Methyl-Coenzyme M reductase (MR) 884.12. Heterodisulfide reductase (HR) 924.13. Methanol methanogenesis-related methyltransferases 934.14. Carbon monoxide dehydrogenase complex 944.15. Acetate activating enzymes 98

5. Key remaining physiological and enzymatic questions 100Acknowledgements 100References 100

Chapter 4. Bioenergetics and transport in methanogens and relatedthermophilic archaeaP. Schonheit 113

Abbreviations 1131. Introduction 1132. Energy substrates 115

2.1. Reduction of CO2 to CH4 1162.2. Reduction of a methyl group to CH4 117

3. Energetics of methanogenesis from CO2/H2 1193.1. Enzymology 119

3.1.1. CO2 reduction to formyl-MFR (formate level) 1193.1.2. Formyl-MFR reduction to methylene-ILtMPT (formaldehyde level) . . 1233.1.3. Methylene-H4MPT conversion to methyl-coenzymeM (methanol level) 1233.1.4. Methyl-coenzyme M (CH3-S-C0M) reduction to methane 124

3.2. Sites of energy coupling 1243.2.1. General aspects 124

3.2.1.1. Growth yields and ATP gains 1253.2.1.2. Mechanism of ATP synthesis 1253.2.1.3. Thermodynamics of partial reactions 126

3.2.2. Methyl-coenzyme M reduction to CH4 - site of primary AjlH+ generationand of ATP synthesis 1273.2.2.1. Heterodisulfide (CoM-S-S-HTP) reduction - coupled to primary

H+ translocation 1283.2.2.2. ATP synthase/ATPase 1313.2.2.3. Misleading concepts of ATP synthesis 132

3.2.3. Methylene-H4MPT conversion to methyl-coenzyme M - site of primaryA/iNa+ generation 1333.2.3.1. Methyl-tLtMPT: coenzymeM methyltransferase - coupled to

primary Na+ translocation 1333.2.4. CO2 reduction to methylene-H4MPT - site of primary A/iNa+

consumption 1353.2.4.1. Formaldehyde oxidation to CO2 - coupled to primary Na+

extrusion 1353.2.4.2. CO2 reduction to methylene-H4MPT - coupled to Na+ uptake 136

3.3. Role of the Na+/H+ antiporter in CO2 reduction to CH4 1373.3.1. Na+/H+ antiporter 1383.3.2. Role of the Na+/H+ antiporter 1383.3.3. Primary cycles of Na+ and H+ 139

3.4. Energetics of CH4 formation from formate 1393.5. Energetics of CH4 formation from CO2 reduction by alcohols 1393.6. Energetics of CO2 reduction to CH4 by methanogens versus CO2 reduction to

acetate by acetogens 1414. Energetics of methanogenesis from methanol 143

4.1. Enzymology 1434.2. Energetics 144

4.2.1. Role of the Na+/H+ antiporter 1454.2.2. Role of methyltransferase 1454.2.3. Role of cytochromes 1474.2.4. Growth yields 147

4.3. Energetics of CH4 formation from methylamines 1475. Energetics of methanogenesis from acetate 147

5.1. Enzymology 1475.2. Sites of energy coupling 148

5.2.1. CH3-S-C0M reduction to CH4 1485.2.2. CO oxidation to CO2 1495.2.3. CH3-H4MPT:H-S-CoM methyltransferase 151

5.3. Acetate fermentation in Methanothrix soehngenii 1536. Energetics of pyruvate catabolism 153

6.1. Methanogenesis from pyruvate 1536.2. Acetate formation from pyruvate in the absence of methanogenesis 154

7. Concluding remarks on energetics 155

8. Transport in methanogens 1568.1. H-S-CoM, CH3-S-C0M 1568.2. Amino acids 1578.3. Nickel 1578.4. Potassium 1578.5. Phosphate 158

9. Energetics of Archaeoglobus and Pyrococcus - non-methanogenic thermophilic archaearelated to methanogens 1589.1. Energetics of Archaeoglobus fulgidus 159

9.1.1. Acetyl-CoA oxidation to CO2 via a modified acetyl-CoA/carbon monox-ide dehydrogenase pathway 159

9.2. Energetics of Pyrococcus furiosus 1619.2.1. Novel sugar degradation pathway in Pyrococcus furiosus 1629.2.2. Sugar degradation to acetate, CO2 and H2 via a novel fermentation

pathway 1629.2.3. Open questions 164

Acknowledgements 164References 164

Chapter 5. Signal transduction in halobacteriaD. Oesterhelt and W. Marwan 173

1. Introduction 1731.1. General 1731.2. Photoreceptors 1731.3. Movement 1741.4. Signal transduction 174

2. Flagellar motor and motility 1752.1. Mode of movement 1752.2. Filament and flagellins 1762.3. Motor switching 176

3. Signal transduction pathway 1773.1. Basic observations 1773.2. Signal formation 1783.3. Identification of a switch factor 1803.4. Light-induced release of fumarate 1803.5. Methyl-accepting taxis proteins 1813.6. Cyclic GMP 182

4. The photoreceptors 1834.1. Spectroscopic and biochemical properties 1834.2. The physiology of photoreception 183

Acknowledgement 185References 185

Chapter 6. Ion transport rhodopsins (bacteriorhodopsin and halo-rhodopsin): Structure and functionJ.K. Lanyi 189

1. Introduction 189

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2. Structure 1903. Chromophore 1934. Properties of the Schiff base 1955. Photoreactions and photocycles 1966. Transport mechanism 1997. Energetics and coupling 2018. Summary 202References 203

Chapter 7. Proteins of extreme thermophilesR. Hensel 209

Abbreviations 2091. Introduction 2092. Features of protein thermoadaptation in archaea 212

2.1. How structurally different are proteins from the extreme thermophiles ascompared to their mesophilic counterparts? 212

2.2. How are the proteins from thermophiles growing at or above the boiling pointof water stabilized towards heat-induced covalent modifications of the peptidechain? 214

2.3. Extrinsic factors stabilizing the native state of proteins at high temperatures . . 2153. Proteins with suggested thermoadaptive functions 215

3.1. Proteins which presumably protect DNA 2163.2. Proteins which presumably protect proteins 216

4. Proteins with biotechnological potential 2165. Conclusions 218Acknowledgement 218References 218

Chapter 8. Cell envelopes of archaea: Structure and chemistry0. Kandler and H. Konig 223

1. Introduction 2232. Structure and chemistry of cell walls of gram-positive archaea 223

2.1. Methanobacteriales and Methanopyrus 2232.1.1. Morphology 2232.1.2. Chemical structure and modifications of pseudomurein 2242.1.3. Secondary and tertiary structure of pseudomurein 2282.1.4. Lysis of pseudomurein 2292.1.5. Biosynthesis of the pseudomurein 2292.1.6. Biological activity of pseudomurein 2312.1.7. Chemical structure and biosynthesis of the S-layer glycoprotein of

Methanothermus fervidus 2312.2. Methanosarcina 232

2.2.1. Morphology 2322.2.2. Chemical structure of methanochondroitin 2322.2.3. Autolysis 2332.2.4. Biosynthesis of methanochondroitin 235

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2.3. Halococcus 2362.3.1. Morphology 2362.3.2. Chemical structure of halococcal heteropolysaccharide 236

2.4. Natronococcus 2372.4.1. Morphology 2372.4.2. Chemical composition of the natronococcal "glycosaminoglycan" . . . . 237

3. Structure and chemistry of cell envelopes of gram-negative archaea 2393.1. Proteinaceous sheaths 239

3.1.1. Methanospirillum hungatei 2393.1.2. Methanothrix concilii (recently renamed Methanosaeta concilii) 240

3.2. S-layers of gram-negative methanogenic rods and cocci 2423.3. S-layers of gram-negative halobacteria 243

3.3.1. Chemical structure 2433.3.2. Biosynthesis 2453.3.3. Halobacterial versus eukaryotic glycoproteins 2463.3.4. Three-dimensional structure 246

3.4. S-layers of Archaeoglobus 2473.5. S-layers of sulfur-metabolizing hyperthermophilic archaea 248

4. Surface structure of archaea without cell envelopes 2525. Concluding remarks 252References 255

Chapter 9. Membrane lipids of archaeaM. Kates 261

1. Introduction 2612. "Core" archaeal lipids 262

2.1. Diphytanylglycerol diether (archaeol) and variants 2622.2. Dibiphytanyldiglycerol tetraether (caldarchaeol) and variants 265

3. Polar lipids 2653.1. Extreme halophiles 265

3.1.1. Phospholipids 2653.1.2. Glycolipids i 2663.1.3. Taxonomic relations 267

3.2. Methanogens 2693.2.1. Methanobacteriaceae 2703.2.2. Methanomicrobiaceae 2723.2.3. Methanococcaceae 2723.2.4. Methanosarcinaceae 2723.2.5. Taxonomic relations 273

3.3. Extreme thermophiles 2733.3.1. Thermoplasmatales 2743.3.2. Sulfolobales 2753.3.3. Thermoproteales 2763.3.4. Thermococcales 2773.3.5. Taxonomic "relations 277

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4. Biosynthetic pathways 2784.1. Archaeol lipid cores 2794.2. Archaeol phospholipids 283

4.2.1. In extreme halophiles - 2834.2.2. In methanogens 283

4.3. Archaeol glycolipids 2844.4. Caldarchaeol phospholipids, glycolipids and phosphoglycolipids 285

4.4.1. In methanogens 2854.4.2. In thermoacidophiles 286

5. Membrane function of archaeal lipids 2875.1. Archaeol-derived lipids in extreme halophiles 2875.2. Caldarchaeol-derived lipids in methanogens and thermoacidophiles 288

6. Evolutionary considerations and conclusions 289Acknowledgement 291Note added in proof 291References 292

Chapter 10. The membrane-bound enzymes of the archaeaL.I. Hochstein 297

1. Introduction 2972. Methods 298

2.1. Preparation of membranes 2982.2. Isolation of membrane components 298

3. The ATPases 2993.1. The ATPases of the methanogens 3003.2. The ATPases of Sulfolobus 3023.3. The ATPases of Thermoplasma 3043.4. The ATPases of the extreme halophiles 304

4. The electron transport system 3084.1. NADH oxidases 308

4.1.1. The NADH oxidase of Sulfolobus 3084.1.2. The NADH oxidase of the extreme halophiles 308

4.2. NADH dehydrogenases 3094.2.1. NADH dehydrogenase from Sulfolobus 3094.2.2. NADH dehydrogenase of extreme halophiles 309

4.3. Succinic dehydrogenases 3114.3.1. Succinic dehydrogenases of Sulfolobus 3114.3.2. Succinate dehydrogenase from the extreme halophiles 311

4.4. The cytochromes 3124.4.1. The cytochromes of the methanogens 3124.4.2. The cytochromes of Sulfolobus 3124.4.3. The cytochromes of Thermoplasma 3134.4.4. The cytochromes of the extreme halophiles 314

5. Hydrogenases 3165.1. Hydrogenases'in methanogens 3165.2. Hydrogenase in Pyrodictium 316

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6. The enzymes of denitrification 3176.1. Nitrate reductase 3176.2. Nitrite reductase activity 318

7. Summary 318References 319

Chapter 11. Chromosome structure, DNA topoisomerases, andDNA polymerases in archaebacteria (archaea)P. Forterre and C. Elie 325

1. Introduction 3252. Chromosome structure 326

2.1. Genome size and organization 3262.2. Putative histone-like proteins and nucleosomes 327

2.2.1. The protein HTa 3272.2.2. The protein MCI 3292.2.3. The protein HMf 3292.2.4. Putative nucleosomal organization 331

2.3. DNA stability in hyperthermophiles : 3313. DNA topoisomerases and DNA topology 333

3.1. Reverse gyrase 3363.1.1. Discovery 3363.1.2. Biochemical characterization 3373.1.3. Mechanistic studies 3373.1.4. Primary structure 3383.1.5. Mechanism of reverse gyration 3383.1.6. Distribution of reverse gyrase in the living world 3393.1.7. Putative roles of reverse gyrase 340

3.2. Other DNA topoisomerases in thermophilic archaebacteria 3423.2.1. Sulfolobus type II DNA topoisomerase 3423.2.2. ATP-independent DNA topoisomerases 343

3.3. Topological state of the DNA in extremely thermophilic archaebacteria 3433.4. DNA topology in halophilic archaebacteria 346

3.4.1. Sensitivity of halobacteria to DNA topoisomerase II inhibitors 3463.4.2. Gene structure and primary sequence of a halobacterial type II DNA topo-

isomerase 3473.4.3. Biological roles of type II DNA topoisomerase in halophilic archaebacteria 349

3.5. An overview of DNA topology in archaebacteria 3494. DNA polymerases 351

4.1. Sensitivity of archaebacteria to aphidicolin 3524.2. DNA polymerases from sulfothermophiles and methanogens 353

4.2.1. Aphidicolin-sensitive DNA polymerases 3534.2.2. Aphidicolin-resistant DNA polymerases 355

4.3. DNA polymerases from halophiles 3564.4. Conclusions 356

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5. General discussion 3575.1. Future prospects 3575.2. Evolutionary considerations 358

5.2.1. Eukaryotic versus eubacterial features of archaebacteria . - 3585.2.2. The root of the tree of life and other phylogenetic problems 3595.2.3. The last common universal ancestor 360

Acknowledgements 360References 361

Chapter 12. Transcription in archaeaW. Zillig, P. Palm, H.-P. Klenk, D. Langer, U. Hudepohl, J. Hain,M. Lanzendorfer and I. Holz 367

Abbreviations 3671. Introduction 3672. DNA-dependent RNA polymerase 369

2.1. Composition 3692.2. Organization of RNAP component genes 3712.3. Similarities between sequences of RNAP components 3732.4. The phylogeny of RNAP components 3732.5. The structure of the RNAP of S. acidocaldarius 377

3. Transcription signals: Promoters and terminators 3793.1. Promoters 3793.2. Terminators 383

4. In vitro transcription systems 3845. Control of transcription 3846. Summary 386Note added in proof 386References 386

Chapter 13. Translation in archaeaR. Amils, P. Cammarano and P. Londei 393

1. Introduction 3932. Structure of translational components 394

2.1. Transfer RNAs and aminoacyl-tRNA synthetases 3942.2. Messenger RNAs 3942.3. Messenger RNA-ribosome interaction 3952.4. Polypeptide chain initiation 3962.5. Elongation factors 396

2.5.1. Elongation factor sequences 3962.5.2. Elongation factor gene order 398

2.6. Archaeal ribosomes. Halotolerance and heat-stability 4002.6.1. Ribosomal subunit interaction 4022.6.2. Ribosome mass and composition 4022.6.3. Ribosome shape 405

2.7. In vitro reconstruction of ribosomal subunits 4072.7.1. Reconstruction of Sulfolobus 50S subunits 4072.7.2. Reconstitution of Haloferax 50S subunits 408

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2.8. Protein targeting and signal recognition in archaea 4103. In vitro translation systems 411

3.1. Translation systems from halophilic archaea 4113.2. Translation systems from methanogenic archaea 4123.3. Translation systems from sulfur-dependent archaea 4123.4. Peptidyltransferase assay systems 4133.5. Distinctness of euryarchaeal and crenarchaeal translation systems 415

4. Sensitivity of archaea to protein synthesis inhibitors 4164.1. Ribosome-targeted inhibitors: in vivo assays 4174.2. Ribosome-targeted inhibitors: in vitro assays 4174.3. Structural correlates of sensitivity to ribosome-targeted drugs 4204.4. Elongation factor-targeted inhibitors 425

4.4.1. EF-2- and EF-G-targeted inhibitors 4264.4.2. EF-la- and EF-Tu-targeted inhibitors 427

4.5. Phylogeny inference from antibiotic sensitivity spectra 4275. Interchangeability of translational components 428

5.1. Interchangeability of ribosomal subunits 4285.2. Interchangeability of elongation factors 4295.3. Interchangeability of ribosomal RNAs and proteins 429

5.3.1. Interchangeability of 5S RNAs 4305.3.2. Interchangeability of 50S subunit proteins 430

6. Conclusions 430References 432

Chapter 14. The structure, function and evolution ofarchaeal ribosomesC. Ramirez, A.K.E. Kopke, D-C. Yang, T. Boeckh and A.T. Matheson . 439

1. Introduction 4392. The archaeal ribosomes 4393. Archaeal ribosomal RNA 441

3.1. Gene organization 4413.2. rRNA structure and function 443

3.2.1. Functional domains \ 4443.2.1.1. The peptidyltransferase center 4443.2.1.2. The GTPase center 444

4. Structure of archaeal ribosomal proteins 4464.1. Nomenclature of ribosomal proteins 4464.2. Comparison of the archaeal r-proteins with those from bacteria and eucarya . . 4464.3. The L2 r-protein family 4514.4. The stalk protuberance in the large ribosomal subunit (r-proteins L12/L10) . . . 4514.5. Interchangeability of ribosomal components from different organisms 454

5. Archaeal ribosomal protein genes 4545.1. Gene organization 4545.2. Transcription 4555.3. Translation signals 4555.4. Regulation 457

6. Evolution of the ribosome 458Acknowledgements 460References 460

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Chapter 15. Halobacterial genes and genomesL.C. Schalkwyk 467

Abbreviations - 4671. Introduction 4672. Halobacterial genomes 468

2.1. Size 4682.2. Plasmids 4692.3. Inhomogeneity of composition 4702.4. Repeated sequences and instability 471

3. Genetics 4733.1. Physical mapping: Introduction 4743.2. Clues from comparison of bacterial genetic maps 4743.3. The Haloferax volcanii map 4753.4. Genes and operons 478

3.4.1. Ribosomal RNA genes 4793.4.2. Transfer RNA genes 4803.4.3. 7S RNA 4803.4.4. RNaseP RNA 4813.4.5. Bacteriorhodopsin 4813.4.6. Halorhodopsin 4823.4.7. Sensory rhodopsins 4833.4.8. Gas-vesicle proteins 4833.4.9. Cell surface glycoprotein 4843.4.10. Flagellins 4843.4.11. Superoxide dismutase 4853.4.12. Dihydrofolate reductase 4853.4.13. DNA gyrase 4863.4.14. Photolyase 4863.4.15. Bacteriophage $H 4873.4.16. H+ ATPase 4873.4.17. Histidinol-phosphate aminotransferase 4873.4.18. 3-Hydroxy-3-methylglutaryl-coenzyme A reductase 4883.4.19. Tryptophan biosynthesis 4883.4.20. Ribosomal proteins 4883.4.21. Elongation factors 4893.4.22. RNA polymerase 489

4. Future directions 490References 491

Chapter 16. Structure and function ofmethanogen genesJ.R. Palmer and J.N. Reeve 497

Abbreviations 4971. Introduction 497

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2. Genes encoding enzymes involved in methanogenesis 5002.1. Methyl-coenzyme M reductase (MR) 5002.2. Hydrogenases and ferredoxins 5032.3. Formate dehydrogenase (FDH) 5042.4. Formylmethanofuran:tetrahydromethanopterinformyltransferase (FTR) 5052.5. Carbon-monoxide dehydrogenase (CODH) and acetyl-coenzyme A synthetase

(ACS) 5063. Amino-acid and purine biosynthetic genes 507

3.1. Histidine 5073.2. Arginine 5073.3. Proline and ISM1 5083.4. Tryptophan 5083.5. Glutamine 5093.6. Adenine 510

4. Transcription and translation machinery genes 5104.1. Stable RNA genes 510

4.1.1. tRNA genes 5104.1.2. rRNA genes 5114.1.3. 7S RNA genes 512

4.2. Genes encoding RNA polymerases, ribosomal proteins and elongation factors . 5124.3. Aminoacyl-tRNA synthetase 514

5. Nitrogen fixation genes 5156. Genes encoding metabolic enzymes 516

6.1. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) 5166.2. L-Malate dehydrogenase (MDH) 5176.3. 3-Phosphoglycerate kinase (PGK) 5176.4. ATPases 5186.5. Superoxide dismutase 5186.6. S-adenosyl-L-methionine:uroporphyrinogenIII methyltransferase (SUMT) . . . . 519

7. Chromosomal proteins 5208. Surface-layer glycoproteins 5209. Flagellins 52110. Gene regulation and genetics :. . 521

10.1. Regulated systems of gene expression \. 52110.2. Transformation systems 522

11. Summary 523References 523

Chapter 17. Archaeal hyperthermophile genesJ.Z. Dalgaard and R.A. Garrett 535

1. Introduction 5352. Gene sequences 5353. Nucleotide composition and optimal growth temperature 5364. Gene organization 5435. Transcriptional signals • 545

5.1. Promoter regions 5455.2. Terminators 549

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6. Translational signals 5516.1. Initiation 5516.2. Codon usage 5536.3. Termination 553

7. Phylogenetie considerations 5578. Summary 558Acknowledgements 559References 559

EpilogueWE Doolittle 565

Introduction 5651. Life's deepest branchings 5652. The coherence of the archaea 5663. Rooting the universal tree 5674. Implications of the root for eucarya 5675. Looking for "pre-adaptations" in archaea 5686. More courageous scenarios 5697. The need for caution and more data 5698. Archaea here and now 570References 570

Index 573