The biochemistry of archaea (archaebacteria):
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| Format: | Book |
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| Language: | English |
| Published: |
Amsterdam [u.a.]
Elsevier
1993
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| Series: | New comprehensive biochemistry
26 |
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Item Description: | Literaturangaben |
| Physical Description: | XLVIII, 582 S. Ill., graph. Darst. |
| ISBN: | 0444817131 |
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| 245 | 1 | 0 | |a The biochemistry of archaea (archaebacteria) |c ed. M. Kates ... |
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| adam_text | THE BIOCHEMISTRY OF ARCHAEA (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
1993 ELSEVFFIR AMSTERDAM * LONDON * NEW YORK * TOKYO CONTENTS PREFACE V
INTRODUCTION. THE ARCHAEA: THEIR HISTORY AND SIGNIFICANCE CARL R. WOESE
VII 1. INTRODUCTION VII 2. MICROBIOLOGY S CHANGING EVOLUTIONARY
PERSPECTIVE XI 3. A MOLECULAR DEFINITION OF THE THREE DOMAINS XV 4.
ARCHAEAL PHYLOGENETIC RELATIONSHIPS XXI 5. THE NEW MICROBIOLOGY XXV
ACKNOWLEDGMENT XXVII REFERENCES XXVII LIST OF CONTRIBUTORS XXXI CHAPTER
1. CENTRAL METABOLISM OF THE ARCHAEA M.J. DANSON 1 1. INTRODUCTION 1
1.1. CENTRAL METABOLISM 1 1.2. CENTRAL METABOLISM IN EUKARYOTES AND
EUBACTERIA : 1 2. HEXOSE CATABOLISM IN THE ARCHAEA 2 2.1. THE MODIFIED
ENTNER-DOUDOROFF PATHWAY OF THE HALOPHILES 2 2.2. THE NON-PHOSPHORYLATED
PATHWAY OF THE THERMOPHILES 5 2.3. THE GLYCOLYTIC PATHWAY OF THE
METHANOGENS 7 2.4. GLUCONEOGENESIS 7 2.5. THE PENTOSE-PHOSPHATE PATHWAY
8 3. PYRUVATE OXIDATION TO ACETYL-COA IN THE ARCHAEA 8 3.1. PYRUVATE
OXIDOREDUCTASES 8 3.2. COMPARISON WITH THE EUKARYOTIC AND EUBACTERIAL
ENZYMES 9 3.3. DIHYDROLIPOAMIDE DEHYDROGENASE 10 4. THE CITRIC ACID
CYCLE IN THE ARCHAEA 11 4.1. THE OXIDATIVE CITRIC ACID CYCLE 11 4.2. THE
REDUCTIVE CITRIC ACID CYCLE 12 4.3. PARTIAL CITRIC ACID CYCLES 13 4.4.
OTHER PATHWAYS OF ACETYL-COA METABOLISM I 13 5. AMINO ACID AND LIPID
METABOLISM IN THE ARCHAEA 14 6. EVOLUTION OF CENTRAL METABOLISM 15 6.1.
HEXOSE CATABOLISM 15 6.2. PYRUVATE OXIDATION TO ACETYL-COA 17 6.3. THE
CITRIC ACID CYCLE 17 7. COMPARATIVE ENZYMOLOGY OF CENTRAL METABOLISM 18
7.1. THE ENZYMES AS MOLECULAR CHRONOMETERS 18 7.2. CITRATE SYNTHASE 19
7.2.1. THE COMPARATIVE ENZYMOLOGY OF CITRATE SYNTHASES 19 7.2.2.
ARCHAEBACTERIAL CITRATE SYNTHASES 19 8. CONCLUSIONS AND PERSPECTIVES 20
ACKNOWLEDGEMENTS 20 NOTE ADDED IN PROOF 21 REFERENCES 21 CHAPTER 2.
BIOENERGETICS OF EXTREME HALOPHILES V.P. SKULACHEV . 25 1. INTRODUCTION
25 2. A GENERAL SCHEME OF ENERGY TRANSDUCTION IN EXTREME HALOPHILES 25
3. BACTERIORHODOPSIN AND HALORHODOPSIN 27 3.1. TRANSMEMBRANE CHARGE
DISPLACEMENT 27 3.2. INVOLVEMENT IN PHOTORECEPTION 30 4. RESPIRATORY
CHAIN 32 5. ARGININE FERMENTATION 33 6. H + -ATP-SYNTHASE 33 7.
FORMATION OF K + /NA + GRADIENTS. A/I H + BUFFERING 34 8. NA + ,
METABOLITE SYMPORTS 35 9. A FLAGELLAR MOTOR 36 10. SOME PROSPECTS FOR
FUTURE RESEARCH 37 REFERENCES 37 CHAPTER 3. BIOCHEMISTRY OF
METHANOGENESIS L. DANIELS 41 1. INTRODUCTION 41 2. NOVEL COENZYMES 43
2.1. GENERAL 43 2.2. THE 5-DEAZAFLAVIN, F420 45 2.3. METHANOFURAN (MF)
47 2.4. TETRAHYDROMETHANOPTERIN (H4MPT) 48 2.5. COENZYMEM 50 2.6.
COBAMIDES - 51 2.7. F430 51 2.8. 7-MERCAPTOHEPTANOYLTHREONINE PHOSPHATE
(HSHTP) 53 3. THE PATHWAYS AND BIOCHEMISTRY OF METHANOGENESIS 53 3.1.
METHANOGENESIS FROM CO2 53 3.1.1. REDUCTION OF CO 2 53 3.1.2. THE RPG
EFFECT 57 3.1.3. SOURCE OF ELECTRONS 57 3.2. METHANOGENESIS FROM
METHANOL 58 3.2.1. REDUCTION OF METHANOL 58 3.2.2. OXIDATION OF METHANOL
59 3.2.3. ELECTRON TRANSFER 60 3.2.4. METHANOGENESIS FROM METHYLAMINES
61 3.3. METHANOGENESIS FROM ACETATE 61 3.3.1. TRANSPORT OF ACETATE INTO
THE CELL 61 3.3.2. ACTIVATION OF ACETATE 61 3.3.3. CLEAVAGE OF
ACETYL-COA AND CH3-C0M FORMATION 62 3.3.4. REDUCTION OF CH3-C0M TO CH 4
65 3.3.5. ELECTRON TRANSFER 65 4. ENZYMES INVOLVED IN METHANOGENESIS 66
4.1. GENERAL 66 4.2. HYDROGENASE AND NON-CATALYTIC REDOX PROTEINS SUCH
AS FERREDOXIN AND CYTOCHROMES 66 4.2.1. THE METHYLVIOLOGEN-REDUCING
HYDROGENASE (MVH) 68 4.2.2. REDOX-ACTIVE PROTEINS: FERREDOXIN,
CYTOCHROMES, AND OTHERS 69 4.2.3. THE F42O-REDUCING HYDROGENASE (FRH) 70
4.3. ALCOHOL DEHYDROGENASE (ADH) 72 4.4. FORMATE DEHYDROGENASE 73 4.5.
FORMYLMETHANOFURAN DEHYDROGENASE 75 4.6.
FORMYLMETHANOFURANRTETRAHYDROMETHANOPTERIN FORMYLTRANSFERASE 78 4.7. 7V
5 ,./V 10 -METHENYLTETRAHYDROMETHANOPTERIN CYCLOHYDROLASE 79 4.8.
METHYLENETETRAHYDROMETHANOPTERIN DEHYDROGENASE 82 4.9.
METHYLENETETRAHYDROMETHANOPTERIN REDUCTASE 85 4.10.
METHYLTETRAHYDROMETHANOPTERIN:COM METHYLTRANSFERASE 87 4.11.
METHYL-COENZYME M REDUCTASE (MR) 88 4.12. HETERODISULFIDE REDUCTASE (HR)
92 4.13. METHANOL METHANOGENESIS-RELATED METHYLTRANSFERASES 93 4.14.
CARBON MONOXIDE DEHYDROGENASE COMPLEX 94 4.15. ACETATE ACTIVATING
ENZYMES 98 5. KEY REMAINING PHYSIOLOGICAL AND ENZYMATIC QUESTIONS 100
ACKNOWLEDGEMENTS 100 REFERENCES 100 CHAPTER 4. BIOENERGETICS AND
TRANSPORT IN METHANOGENS AND RELATED THERMOPHILIC ARCHAEA P. SCHONHEIT
113 ABBREVIATIONS 113 1. INTRODUCTION 113 2. ENERGY SUBSTRATES 115 2.1.
REDUCTION OF CO2 TO CH 4 116 2.2. REDUCTION OF A METHYL GROUP TO CH4 117
3. ENERGETICS OF METHANOGENESIS FROM CO2/H2 119 3.1. ENZYMOLOGY 119
3.1.1. CO 2 REDUCTION TO FORMYL-MFR (FORMATE LEVEL) 119 3.1.2.
FORMYL-MFR REDUCTION TO METHYLENE-ILTMPT (FORMALDEHYDE LEVEL) .. 123
3.1.3. METHYLENE-H4MPT CONVERSION TO METHYL-COENZYMEM (METHANOL LEVEL)
123 3.1.4. METHYL-COENZYME M (CH3-S-C0M) REDUCTION TO METHANE 124 3.2.
SITES OF ENERGY COUPLING 124 3.2.1. GENERAL ASPECTS 124 3.2.1.1. GROWTH
YIELDS AND ATP GAINS 125 3.2.1.2. MECHANISM OF ATP SYNTHESIS 125
3.2.1.3. THERMODYNAMICS OF PARTIAL REACTIONS 126 3.2.2. METHYL-COENZYME
M REDUCTION TO CH4 - SITE OF PRIMARY AJLH + GENERATION AND OF ATP
SYNTHESIS 127 3.2.2.1. HETERODISULFIDE (COM-S-S-HTP) REDUCTION - COUPLED
TO PRIMARY H + TRANSLOCATION 128 3.2.2.2. ATP SYNTHASE/ATPASE 131
3.2.2.3. MISLEADING CONCEPTS OF ATP SYNTHESIS 132 3.2.3. METHYLENE-H4MPT
CONVERSION TO METHYL-COENZYME M - SITE OF PRIMARY A/INA + GENERATION 133
3.2.3.1. METHYL-TLTMPT: COENZYMEM METHYLTRANSFERASE - COUPLED TO PRIMARY
NA + TRANSLOCATION 133 3.2.4. CO2 REDUCTION TO METHYLENE-H4MPT - SITE OF
PRIMARY A/INA + CONSUMPTION 135 3.2.4.1. FORMALDEHYDE OXIDATION TO CO2 -
COUPLED TO PRIMARY NA + EXTRUSION 135 3.2.4.2. CO 2 REDUCTION TO
METHYLENE-H 4 MPT - COUPLED TO NA + UPTAKE 136 3.3. ROLE OF THE NA + /H
+ ANTIPORTER IN CO 2 REDUCTION TO CH 4 137 3.3.1. NA + /H + ANTIPORTER
138 3.3.2. ROLE OF THE NA + /H + ANTIPORTER 138 3.3.3. PRIMARY CYCLES OF
NA + AND H + 139 3.4. ENERGETICS OF CH4 FORMATION FROM FORMATE 139 3.5.
ENERGETICS OF CH4 FORMATION FROM CO2 REDUCTION BY ALCOHOLS 139 3.6.
ENERGETICS OF CO2 REDUCTION TO CH4 BY METHANOGENS VERSUS CO2 REDUCTION
TO ACETATE BY ACETOGENS 141 4. ENERGETICS OF METHANOGENESIS FROM
METHANOL 143 4.1. ENZYMOLOGY 143 4.2. ENERGETICS 144 4.2.1. ROLE OF THE
NA + /H + ANTIPORTER 145 4.2.2. ROLE OF METHYLTRANSFERASE 145 4.2.3.
ROLE OF CYTOCHROMES 147 4.2.4. GROWTH YIELDS 147 4.3. ENERGETICS OF CH4
FORMATION FROM METHYLAMINES 147 5. ENERGETICS OF METHANOGENESIS FROM
ACETATE 147 5.1. ENZYMOLOGY 147 5.2. SITES OF ENERGY COUPLING 148 5.2.1.
CH3-S-C0M REDUCTION TO CH 4 148 5.2.2. CO OXIDATION TO CO 2 149 5.2.3.
CH 3 -H 4 MPT:H-S-COM METHYLTRANSFERASE 151 5.3. ACETATE FERMENTATION IN
METHANOTHRIX SOEHNGENII 153 6. ENERGETICS OF PYRUVATE CATABOLISM 153
6.1. METHANOGENESIS FROM PYRUVATE 153 6.2. ACETATE FORMATION FROM
PYRUVATE IN THE ABSENCE OF METHANOGENESIS 154 7. CONCLUDING REMARKS ON
ENERGETICS 155 8. TRANSPORT IN METHANOGENS 156 8.1. H-S-COM, CH3-S-C0M
156 8.2. AMINO ACIDS 157 8.3. NICKEL 157 8.4. POTASSIUM 157 8.5.
PHOSPHATE 158 9. ENERGETICS OF ARCHAEOGLOBUS AND PYROCOCCUS -
NON-METHANOGENIC THERMOPHILIC ARCHAEA RELATED TO METHANOGENS 158 9.1.
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 161 9.2.1. NOVEL SUGAR
DEGRADATION PATHWAY IN PYROCOCCUS FURIOSUS 162 9.2.2. SUGAR DEGRADATION
TO ACETATE, CO2 AND H2 VIA A NOVEL FERMENTATION PATHWAY 162 9.2.3. OPEN
QUESTIONS 164 ACKNOWLEDGEMENTS 164 REFERENCES 164 CHAPTER 5. SIGNAL
TRANSDUCTION IN HALOBACTERIA D. OESTERHELT AND W. MARWAN 173 1.
INTRODUCTION 173 1.1. GENERAL 173 1.2. PHOTORECEPTORS 173 1.3. MOVEMENT
174 1.4. SIGNAL TRANSDUCTION 174 2. FLAGELLAR MOTOR AND MOTILITY 175
2.1. MODE OF MOVEMENT 175 2.2. FILAMENT AND FLAGELLINS 176 2.3. MOTOR
SWITCHING 176 3. SIGNAL TRANSDUCTION PATHWAY 177 3.1. BASIC OBSERVATIONS
177 3.2. SIGNAL FORMATION 178 3.3. IDENTIFICATION OF A SWITCH FACTOR 180
3.4. LIGHT-INDUCED RELEASE OF FUMARATE 180 3.5. METHYL-ACCEPTING TAXIS
PROTEINS 181 3.6. CYCLIC GMP 182 4. THE PHOTORECEPTORS 183 4.1.
SPECTROSCOPIC AND BIOCHEMICAL PROPERTIES 183 4.2. THE PHYSIOLOGY OF
PHOTORECEPTION 183 ACKNOWLEDGEMENT 185 REFERENCES 185 CHAPTER 6. ION
TRANSPORT RHODOPSINS (BACTERIORHODOPSIN AND HALO- RHODOPSIN): STRUCTURE
AND FUNCTION J.K. LANYI 189 1. INTRODUCTION 189 XL 2. STRUCTURE 190 3.
CHROMOPHORE 193 4. PROPERTIES OF THE SCHIFF BASE 195 5. PHOTOREACTIONS
AND PHOTOCYCLES 196 6. TRANSPORT MECHANISM 199 7. ENERGETICS AND
COUPLING 201 8. SUMMARY 202 REFERENCES 203 CHAPTER 7. PROTEINS OF
EXTREME THERMOPHILES R. HENSEL 209 ABBREVIATIONS 209 1. INTRODUCTION 209
2. FEATURES OF PROTEIN THERMOADAPTATION IN ARCHAEA 212 2.1. HOW
STRUCTURALLY DIFFERENT ARE PROTEINS FROM THE EXTREME THERMOPHILES AS
COMPARED TO THEIR MESOPHILIC COUNTERPARTS? 212 2.2. HOW ARE THE PROTEINS
FROM THERMOPHILES GROWING AT OR ABOVE THE BOILING POINT OF WATER
STABILIZED TOWARDS HEAT-INDUCED COVALENT MODIFICATIONS OF THE PEPTIDE
CHAIN? 214 2.3. EXTRINSIC FACTORS STABILIZING THE NATIVE STATE OF
PROTEINS AT HIGH TEMPERATURES . . 215 3. PROTEINS WITH SUGGESTED
THERMOADAPTIVE FUNCTIONS 215 3.1. PROTEINS WHICH PRESUMABLY PROTECT DNA
216 3.2. PROTEINS WHICH PRESUMABLY PROTECT PROTEINS 216 4. PROTEINS WITH
BIOTECHNOLOGICAL POTENTIAL 216 5. CONCLUSIONS 218 ACKNOWLEDGEMENT 218
REFERENCES 218 CHAPTER 8. CELL ENVELOPES OF ARCHAEA: STRUCTURE AND
CHEMISTRY 0. KANDLER AND H. KONIG 223 1. INTRODUCTION 223 2. STRUCTURE
AND CHEMISTRY OF CELL WALLS OF GRAM-POSITIVE ARCHAEA 223 2.1.
METHANOBACTERIALES AND METHANOPYRUS 223 2.1.1. MORPHOLOGY 223 2.1.2.
CHEMICAL STRUCTURE AND MODIFICATIONS OF PSEUDOMUREIN 224 2.1.3.
SECONDARY AND TERTIARY STRUCTURE OF PSEUDOMUREIN 228 2.1.4. LYSIS OF
PSEUDOMUREIN 229 2.1.5. BIOSYNTHESIS OF THE PSEUDOMUREIN 229 2.1.6.
BIOLOGICAL ACTIVITY OF PSEUDOMUREIN 231 2.1.7. CHEMICAL STRUCTURE AND
BIOSYNTHESIS OF THE S-LAYER GLYCOPROTEIN OF METHANOTHERMUS FERVIDUS 231
2.2. METHANOSARCINA 232 2.2.1. MORPHOLOGY 232 2.2.2. CHEMICAL STRUCTURE
OF METHANOCHONDROITIN 232 2.2.3. AUTOLYSIS 233 2.2.4. BIOSYNTHESIS OF
METHANOCHONDROITIN 235 XLI 2.3. HALOCOCCUS 236 2.3.1. MORPHOLOGY 236
2.3.2. CHEMICAL STRUCTURE OF HALOCOCCAL HETEROPOLYSACCHARIDE 236 2.4.
NATRONOCOCCUS 237 2.4.1. MORPHOLOGY 237 2.4.2. CHEMICAL COMPOSITION OF
THE NATRONOCOCCAL GLYCOSAMINOGLYCAN .... 237 3. STRUCTURE AND
CHEMISTRY OF CELL ENVELOPES OF GRAM-NEGATIVE ARCHAEA 239 3.1.
PROTEINACEOUS SHEATHS 239 3.1.1. METHANOSPIRILLUM HUNGATEI 239 3.1.2.
METHANOTHRIX CONCILII (RECENTLY RENAMED METHANOSAETA CONCILII) 240 3.2.
S-LAYERS OF GRAM-NEGATIVE METHANOGENIC RODS AND COCCI 242 3.3. S-LAYERS
OF GRAM-NEGATIVE HALOBACTERIA 243 3.3.1. CHEMICAL STRUCTURE 243 3.3.2.
BIOSYNTHESIS 245 3.3.3. HALOBACTERIAL VERSUS EUKARYOTIC GLYCOPROTEINS
246 3.3.4. THREE-DIMENSIONAL STRUCTURE 246 3.4. S-LAYERS OF
ARCHAEOGLOBUS 247 3.5. S-LAYERS OF SULFUR-METABOLIZING HYPERTHERMOPHILIC
ARCHAEA 248 4. SURFACE STRUCTURE OF ARCHAEA WITHOUT CELL ENVELOPES 252
5. CONCLUDING REMARKS 252 REFERENCES 255 CHAPTER 9. MEMBRANE LIPIDS OF
ARCHAEA M. KATES 261 1. INTRODUCTION 261 2. CORE ARCHAEAL LIPIDS 262
2.1. DIPHYTANYLGLYCEROL DIETHER (ARCHAEOL) AND VARIANTS 262 2.2.
DIBIPHYTANYLDIGLYCEROL TETRAETHER (CALDARCHAEOL) AND VARIANTS 265 3.
POLAR LIPIDS 265 3.1. EXTREME HALOPHILES 265 3.1.1. PHOSPHOLIPIDS 265
3.1.2. GLYCOLIPIDS I 266 3.1.3. TAXONOMIC RELATIONS 267 3.2. METHANOGENS
269 3.2.1. METHANOBACTERIACEAE 270 3.2.2. METHANOMICROBIACEAE 272 3.2.3.
METHANOCOCCACEAE 272 3.2.4. METHANOSARCINACEAE 272 3.2.5. TAXONOMIC
RELATIONS 273 3.3. EXTREME THERMOPHILES 273 3.3.1. THERMOPLASMATALES 274
3.3.2. SULFOLOBALES 275 3.3.3. THERMOPROTEALES 276 3.3.4. THERMOCOCCALES
277 3.3.5. TAXONOMIC RELATIONS 277 XLII 4. BIOSYNTHETIC PATHWAYS 278
4.1. ARCHAEOL LIPID CORES 279 4.2. ARCHAEOL PHOSPHOLIPIDS 283 4.2.1. IN
EXTREME HALOPHILES - 283 4.2.2. IN METHANOGENS 283 4.3. ARCHAEOL
GLYCOLIPIDS 284 4.4. CALDARCHAEOL PHOSPHOLIPIDS, GLYCOLIPIDS AND
PHOSPHOGLYCOLIPIDS 285 4.4.1. IN METHANOGENS 285 4.4.2. IN
THERMOACIDOPHILES 286 5. MEMBRANE FUNCTION OF ARCHAEAL LIPIDS 287 5.1.
ARCHAEOL-DERIVED LIPIDS IN EXTREME HALOPHILES 287 5.2.
CALDARCHAEOL-DERIVED LIPIDS IN METHANOGENS AND THERMOACIDOPHILES 288 6.
EVOLUTIONARY CONSIDERATIONS AND CONCLUSIONS 289 ACKNOWLEDGEMENT 291 NOTE
ADDED IN PROOF 291 REFERENCES 292 CHAPTER 10. THE MEMBRANE-BOUND ENZYMES
OF THE ARCHAEA L.I. HOCHSTEIN 297 1. INTRODUCTION 297 2. METHODS 298
2.1. PREPARATION OF MEMBRANES 298 2.2. ISOLATION OF MEMBRANE COMPONENTS
298 3. THE ATPASES 299 3.1. THE ATPASES OF THE METHANOGENS 300 3.2. THE
ATPASES OF SULFOLOBUS 302 3.3. THE ATPASES OF THERMOPLASMA 304 3.4. THE
ATPASES OF THE EXTREME HALOPHILES 304 4. THE ELECTRON TRANSPORT SYSTEM
308 4.1. NADH OXIDASES 308 4.1.1. THE NADH OXIDASE OF SULFOLOBUS 308
4.1.2. THE NADH OXIDASE OF THE EXTREME HALOPHILES 308 4.2. NADH
DEHYDROGENASES 309 4.2.1. NADH DEHYDROGENASE FROM SULFOLOBUS 309 4.2.2.
NADH DEHYDROGENASE OF EXTREME HALOPHILES 309 4.3. SUCCINIC
DEHYDROGENASES 311 4.3.1. SUCCINIC DEHYDROGENASES OF SULFOLOBUS 311
4.3.2. SUCCINATE DEHYDROGENASE FROM THE EXTREME HALOPHILES 311 4.4. THE
CYTOCHROMES 312 4.4.1. THE CYTOCHROMES OF THE METHANOGENS 312 4.4.2. THE
CYTOCHROMES OF SULFOLOBUS 312 4.4.3. THE CYTOCHROMES OF THERMOPLASMA 313
4.4.4. THE CYTOCHROMES OF THE EXTREME HALOPHILES 314 5. HYDROGENASES 316
5.1. HYDROGENASES IN METHANOGENS 316 5.2. HYDROGENASE IN PYRODICTIUM 316
XLIII 6. THE ENZYMES OF DENITRIFICATION 317 6.1. NITRATE REDUCTASE 317
6.2. NITRITE REDUCTASE ACTIVITY 318 7. SUMMARY 318 REFERENCES 319
CHAPTER 11. CHROMOSOME STRUCTURE, DNA TOPOISOMERASES, AND DNA
POLYMERASES IN ARCHAEBACTERIA (ARCHAEA) P. FORTERRE AND C. ELIE 325 1.
INTRODUCTION 325 2. CHROMOSOME STRUCTURE 326 2.1. GENOME SIZE AND
ORGANIZATION 326 2.2. PUTATIVE HISTONE-LIKE PROTEINS AND NUCLEOSOMES 327
2.2.1. THE PROTEIN HTA 327 2.2.2. THE PROTEIN MCI 329 2.2.3. THE PROTEIN
HMF 329 2.2.4. PUTATIVE NUCLEOSOMAL ORGANIZATION 331 2.3. DNA STABILITY
IN HYPERTHERMOPHILES : 331 3. DNA TOPOISOMERASES AND DNA TOPOLOGY 333
3.1. REVERSE GYRASE 336 3.1.1. DISCOVERY 336 3.1.2. BIOCHEMICAL
CHARACTERIZATION 337 3.1.3. MECHANISTIC STUDIES 337 3.1.4. PRIMARY
STRUCTURE 338 3.1.5. MECHANISM OF REVERSE GYRATION 338 3.1.6.
DISTRIBUTION OF REVERSE GYRASE IN THE LIVING WORLD 339 3.1.7. PUTATIVE
ROLES OF REVERSE GYRASE 340 3.2. OTHER DNA TOPOISOMERASES IN
THERMOPHILIC ARCHAEBACTERIA 342 3.2.1. SULFOLOBUS TYPE II DNA
TOPOISOMERASE 342 3.2.2. ATP-INDEPENDENT DNA TOPOISOMERASES 343 3.3.
TOPOLOGICAL STATE OF THE DNA IN EXTREMELY THERMOPHILIC ARCHAEBACTERIA
343 3.4. DNA TOPOLOGY IN HALOPHILIC ARCHAEBACTERIA 346 3.4.1.
SENSITIVITY OF HALOBACTERIA TO DNA TOPOISOMERASE II INHIBITORS 346
3.4.2. GENE STRUCTURE AND PRIMARY SEQUENCE OF A HALOBACTERIAL TYPE II
DNA TOPO- ISOMERASE 347 3.4.3. BIOLOGICAL ROLES OF TYPE II DNA
TOPOISOMERASE IN HALOPHILIC ARCHAEBACTERIA 349 3.5. AN OVERVIEW OF DNA
TOPOLOGY IN ARCHAEBACTERIA 349 4. DNA POLYMERASES 351 4.1. SENSITIVITY
OF ARCHAEBACTERIA TO APHIDICOLIN 352 4.2. DNA POLYMERASES FROM
SULFOTHERMOPHILES AND METHANOGENS 353 4.2.1. APHIDICOLIN-SENSITIVE DNA
POLYMERASES 353 4.2.2. APHIDICOLIN-RESISTANT DNA POLYMERASES 355 4.3.
DNA POLYMERASES FROM HALOPHILES 356 4.4. CONCLUSIONS 356 XLIV 5. GENERAL
DISCUSSION 357 5.1. FUTURE PROSPECTS 357 5.2. EVOLUTIONARY
CONSIDERATIONS 358 5.2.1. EUKARYOTIC VERSUS EUBACTERIAL FEATURES OF
ARCHAEBACTERIA . - 358 5.2.2. THE ROOT OF THE TREE OF LIFE AND OTHER
PHYLOGENETIC PROBLEMS 359 5.2.3. THE LAST COMMON UNIVERSAL ANCESTOR 360
ACKNOWLEDGEMENTS 360 REFERENCES 361 CHAPTER 12. TRANSCRIPTION IN ARCHAEA
W. ZILLIG, P. PALM, H.-P. KLENK, D. LANGER, U. HUDEPOHL, J. HAIN, M.
LANZENDORFER AND I. HOLZ 367 ABBREVIATIONS 367 1. INTRODUCTION 367 2.
DNA-DEPENDENT RNA POLYMERASE 369 2.1. COMPOSITION 369 2.2. ORGANIZATION
OF RNAP COMPONENT GENES 371 2.3. SIMILARITIES BETWEEN SEQUENCES OF RNAP
COMPONENTS 373 2.4. THE PHYLOGENY OF RNAP COMPONENTS 373 2.5. THE
STRUCTURE OF THE RNAP OF S. ACIDOCALDARIUS 377 3. TRANSCRIPTION SIGNALS:
PROMOTERS AND TERMINATORS 379 3.1. PROMOTERS 379 3.2. TERMINATORS 383 4.
IN VITRO TRANSCRIPTION SYSTEMS 384 5. CONTROL OF TRANSCRIPTION 384 6.
SUMMARY 386 NOTE ADDED IN PROOF 386 REFERENCES 386 CHAPTER 13.
TRANSLATION IN ARCHAEA R. AMILS, P. CAMMARANO AND P. LONDEI 393 1.
INTRODUCTION 393 2. STRUCTURE OF TRANSLATIONAL COMPONENTS 394 2.1.
TRANSFER RNAS AND AMINOACYL-TRNA SYNTHETASES 394 2.2. MESSENGER RNAS 394
2.3. MESSENGER RNA-RIBOSOME INTERACTION 395 2.4. POLYPEPTIDE CHAIN
INITIATION 396 2.5. ELONGATION FACTORS 396 2.5.1. ELONGATION FACTOR
SEQUENCES 396 2.5.2. ELONGATION FACTOR GENE ORDER 398 2.6. ARCHAEAL
RIBOSOMES. HALOTOLERANCE AND HEAT-STABILITY 400 2.6.1. RIBOSOMAL SUBUNIT
INTERACTION 402 2.6.2. RIBOSOME MASS AND COMPOSITION 402 2.6.3. RIBOSOME
SHAPE 405 2.7. IN VITRO RECONSTRUCTION OF RIBOSOMAL SUBUNITS 407 2.7.1.
RECONSTRUCTION OF SULFOLOBUS 50S SUBUNITS 407 2.7.2. RECONSTITUTION OF
HALOFERAX 50S SUBUNITS 408 XLV 2.8. PROTEIN TARGETING AND SIGNAL
RECOGNITION IN ARCHAEA 410 3. IN VITRO TRANSLATION SYSTEMS 411 3.1.
TRANSLATION SYSTEMS FROM HALOPHILIC ARCHAEA 411 3.2. TRANSLATION SYSTEMS
FROM METHANOGENIC ARCHAEA 412 3.3. TRANSLATION SYSTEMS FROM
SULFUR-DEPENDENT ARCHAEA 412 3.4. PEPTIDYLTRANSFERASE ASSAY SYSTEMS 413
3.5. DISTINCTNESS OF EURYARCHAEAL AND CRENARCHAEAL TRANSLATION SYSTEMS
415 4. SENSITIVITY OF ARCHAEA TO PROTEIN SYNTHESIS INHIBITORS 416 4.1.
RIBOSOME-TARGETED INHIBITORS: IN VIVO ASSAYS 417 4.2. RIBOSOME-TARGETED
INHIBITORS: IN VITRO ASSAYS 417 4.3. STRUCTURAL CORRELATES OF
SENSITIVITY TO RIBOSOME-TARGETED DRUGS 420 4.4. ELONGATION
FACTOR-TARGETED INHIBITORS 425 4.4.1. EF-2- AND EF-G-TARGETED INHIBITORS
426 4.4.2. EF-LA- AND EF-TU-TARGETED INHIBITORS 427 4.5. PHYLOGENY
INFERENCE FROM ANTIBIOTIC SENSITIVITY SPECTRA 427 5. INTERCHANGEABILITY
OF TRANSLATIONAL COMPONENTS 428 5.1. INTERCHANGEABILITY OF RIBOSOMAL
SUBUNITS 428 5.2. INTERCHANGEABILITY OF ELONGATION FACTORS 429 5.3.
INTERCHANGEABILITY OF RIBOSOMAL RNAS AND PROTEINS 429 5.3.1.
INTERCHANGEABILITY OF 5S RNAS 430 5.3.2. INTERCHANGEABILITY OF 50S
SUBUNIT PROTEINS 430 6. CONCLUSIONS 430 REFERENCES 432 CHAPTER 14. THE
STRUCTURE, FUNCTION AND EVOLUTION OFARCHAEAL RIBOSOMES C. RAMIREZ,
A.K.E. KOPKE, D-C. YANG, T. BOECKH AND A.T. MATHESON . 439 1.
INTRODUCTION 439 2. THE ARCHAEAL RIBOSOMES 439 3. ARCHAEAL RIBOSOMAL RNA
441 3.1. GENE ORGANIZATION 441 3.2. RRNA STRUCTURE AND FUNCTION 443
3.2.1. FUNCTIONAL DOMAINS 444 3.2.1.1. THE PEPTIDYLTRANSFERASE CENTER
444 3.2.1.2. THE GTPASE CENTER 444 4. STRUCTURE OF ARCHAEAL RIBOSOMAL
PROTEINS 446 4.1. NOMENCLATURE OF RIBOSOMAL PROTEINS 446 4.2. COMPARISON
OF THE ARCHAEAL R-PROTEINS WITH THOSE FROM BACTERIA AND EUCARYA . . 446
4.3. THE L2 R-PROTEIN FAMILY 451 4.4. THE STALK PROTUBERANCE IN THE
LARGE RIBOSOMAL SUBUNIT (R-PROTEINS L12/L10) ... 451 4.5.
INTERCHANGEABILITY OF RIBOSOMAL COMPONENTS FROM DIFFERENT ORGANISMS 454
5. ARCHAEAL RIBOSOMAL PROTEIN GENES 454 5.1. GENE ORGANIZATION 454 5.2.
TRANSCRIPTION 455 5.3. TRANSLATION SIGNALS 455 5.4. REGULATION 457 6.
EVOLUTION OF THE RIBOSOME 458 ACKNOWLEDGEMENTS 460 REFERENCES 460 XLVI
CHAPTER 15. HALOBACTERIAL GENES AND GENOMES L.C. SCHALKWYK 467
ABBREVIATIONS - 467 1. INTRODUCTION 467 2. HALOBACTERIAL GENOMES 468
2.1. SIZE 468 2.2. PLASMIDS 469 2.3. INHOMOGENEITY OF COMPOSITION 470
2.4. REPEATED SEQUENCES AND INSTABILITY 471 3. GENETICS 473 3.1.
PHYSICAL MAPPING: INTRODUCTION 474 3.2. CLUES FROM COMPARISON OF
BACTERIAL GENETIC MAPS 474 3.3. THE HALOFERAX VOLCANII MAP 475 3.4.
GENES AND OPERONS 478 3.4.1. RIBOSOMAL RNA GENES 479 3.4.2. TRANSFER RNA
GENES 480 3.4.3. 7S RNA 480 3.4.4. RNASEP RNA 481 3.4.5.
BACTERIORHODOPSIN 481 3.4.6. HALORHODOPSIN 482 3.4.7. SENSORY RHODOPSINS
483 3.4.8. GAS-VESICLE PROTEINS 483 3.4.9. CELL SURFACE GLYCOPROTEIN 484
3.4.10. FLAGELLINS 484 3.4.11. SUPEROXIDE DISMUTASE 485 3.4.12.
DIHYDROFOLATE REDUCTASE 485 3.4.13. DNA GYRASE 486 3.4.14. PHOTOLYASE
486 3.4.15. BACTERIOPHAGE $H 487 3.4.16. H + ATPASE 487 3.4.17.
HISTIDINOL-PHOSPHATE AMINOTRANSFERASE 487 3.4.18.
3-HYDROXY-3-METHYLGLUTARYL-COENZYME A REDUCTASE 488 3.4.19. TRYPTOPHAN
BIOSYNTHESIS 488 3.4.20. RIBOSOMAL PROTEINS 488 3.4.21. ELONGATION
FACTORS 489 3.4.22. RNA POLYMERASE 489 4. FUTURE DIRECTIONS 490
REFERENCES 491 CHAPTER 16. STRUCTURE AND FUNCTION OFMETHANOGEN GENES
J.R. PALMER AND J.N. REEVE 497 ABBREVIATIONS 497 1. INTRODUCTION 497
XLVII 2. GENES ENCODING ENZYMES INVOLVED IN METHANOGENESIS 500 2.1.
METHYL-COENZYME M REDUCTASE (MR) 500 2.2. HYDROGENASES AND FERREDOXINS
503 2.3. FORMATE DEHYDROGENASE (FDH) 504 2.4.
FORMYLMETHANOFURAN:TETRAHYDROMETHANOPTERINFORMYLTRANSFERASE (FTR) 505
2.5. CARBON-MONOXIDE DEHYDROGENASE (CODH) AND ACETYL-COENZYME A
SYNTHETASE (ACS) 506 3. AMINO-ACID AND PURINE BIOSYNTHETIC GENES 507
3.1. HISTIDINE 507 3.2. ARGININE 507 3.3. PROLINE AND ISM1 508 3.4.
TRYPTOPHAN 508 3.5. GLUTAMINE 509 3.6. ADENINE 510 4. TRANSCRIPTION AND
TRANSLATION MACHINERY GENES 510 4.1. STABLE RNA GENES 510 4.1.1. TRNA
GENES 510 4.1.2. RRNA GENES 511 4.1.3. 7S RNA GENES 512 4.2. GENES
ENCODING RNA POLYMERASES, RIBOSOMAL PROTEINS AND ELONGATION FACTORS .
512 4.3. AMINOACYL-TRNA SYNTHETASE 514 5. NITROGEN FIXATION GENES 515 6.
GENES ENCODING METABOLIC ENZYMES 516 6.1. GLYCERALDEHYDE-3-PHOSPHATE
DEHYDROGENASE (GAPDH) 516 6.2. L-MALATE DEHYDROGENASE (MDH) 517 6.3.
3-PHOSPHOGLYCERATE KINASE (PGK) 517 6.4. ATPASES 518 6.5. SUPEROXIDE
DISMUTASE 518 6.6. S-ADENOSYL-L-METHIONINE:UROPORPHYRINOGENIII
METHYLTRANSFERASE (SUMT) .... 519 7. CHROMOSOMAL PROTEINS 520 8.
SURFACE-LAYER GLYCOPROTEINS 520 9. FLAGELLINS 521 10. GENE REGULATION
AND GENETICS :. . 521 10.1. REGULATED SYSTEMS OF GENE EXPRESSION . 521
10.2. TRANSFORMATION SYSTEMS 522 11. SUMMARY 523 REFERENCES 523 CHAPTER
17. ARCHAEAL HYPERTHERMOPHILE GENES J.Z. DALGAARD AND R.A. GARRETT 535
1. INTRODUCTION 535 2. GENE SEQUENCES 535 3. NUCLEOTIDE COMPOSITION AND
OPTIMAL GROWTH TEMPERATURE 536 4. GENE ORGANIZATION 543 5.
TRANSCRIPTIONAL SIGNALS * 545 5.1. PROMOTER REGIONS 545 5.2. TERMINATORS
549 XLVIII 6. TRANSLATIONAL SIGNALS 551 6.1. INITIATION 551 6.2. CODON
USAGE 553 6.3. TERMINATION 553 7. PHYLOGENETIE CONSIDERATIONS 557 8.
SUMMARY 558 ACKNOWLEDGEMENTS 559 REFERENCES 559 EPILOGUE WE DOOLITTLE
565 INTRODUCTION 565 1. LIFE S DEEPEST BRANCHINGS 565 2. THE COHERENCE
OF THE ARCHAEA 566 3. ROOTING THE UNIVERSAL TREE 567 4. IMPLICATIONS OF
THE ROOT FOR EUCARYA 567 5. LOOKING FOR PRE-ADAPTATIONS IN ARCHAEA 568
6. MORE COURAGEOUS SCENARIOS 569 7. THE NEED FOR CAUTION AND MORE DATA
569 8. ARCHAEA HERE AND NOW 570 REFERENCES 570 INDEX 573
|
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| id | DE-604.BV008882095 |
| illustrated | Illustrated |
| indexdate | 2024-07-09T17:26:36Z |
| institution | BVB |
| isbn | 0444817131 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-005875394 |
| oclc_num | 231590799 |
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| owner | DE-703 DE-355 DE-BY-UBR DE-19 DE-BY-UBM DE-29 DE-12 DE-83 DE-11 DE-188 |
| owner_facet | DE-703 DE-355 DE-BY-UBR DE-19 DE-BY-UBM DE-29 DE-12 DE-83 DE-11 DE-188 |
| physical | XLVIII, 582 S. Ill., graph. Darst. |
| publishDate | 1993 |
| publishDateSearch | 1993 |
| publishDateSort | 1993 |
| publisher | Elsevier |
| record_format | marc |
| series | New comprehensive biochemistry |
| series2 | New comprehensive biochemistry |
| spelling | The biochemistry of archaea (archaebacteria) ed. M. Kates ... Amsterdam [u.a.] Elsevier 1993 XLVIII, 582 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier New comprehensive biochemistry 26 Literaturangaben Biochemie (DE-588)4006777-4 gnd rswk-swf Molekularbiologie (DE-588)4039983-7 gnd rswk-swf Archaebakterien (DE-588)4002825-2 gnd rswk-swf Physiologie (DE-588)4045981-0 gnd rswk-swf Archaebakterien (DE-588)4002825-2 s Molekularbiologie (DE-588)4039983-7 s DE-604 Biochemie (DE-588)4006777-4 s Physiologie (DE-588)4045981-0 s Kates, Morris Sonstige oth New comprehensive biochemistry 26 (DE-604)BV000003914 26 GBV Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=005875394&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | The biochemistry of archaea (archaebacteria) New comprehensive biochemistry Biochemie (DE-588)4006777-4 gnd Molekularbiologie (DE-588)4039983-7 gnd Archaebakterien (DE-588)4002825-2 gnd Physiologie (DE-588)4045981-0 gnd |
| subject_GND | (DE-588)4006777-4 (DE-588)4039983-7 (DE-588)4002825-2 (DE-588)4045981-0 |
| title | The biochemistry of archaea (archaebacteria) |
| title_auth | The biochemistry of archaea (archaebacteria) |
| title_exact_search | The biochemistry of archaea (archaebacteria) |
| title_full | The biochemistry of archaea (archaebacteria) ed. M. Kates ... |
| title_fullStr | The biochemistry of archaea (archaebacteria) ed. M. Kates ... |
| title_full_unstemmed | The biochemistry of archaea (archaebacteria) ed. M. Kates ... |
| title_short | The biochemistry of archaea (archaebacteria) |
| title_sort | the biochemistry of archaea archaebacteria |
| topic | Biochemie (DE-588)4006777-4 gnd Molekularbiologie (DE-588)4039983-7 gnd Archaebakterien (DE-588)4002825-2 gnd Physiologie (DE-588)4045981-0 gnd |
| topic_facet | Biochemie Molekularbiologie Archaebakterien Physiologie |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=005875394&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| volume_link | (DE-604)BV000003914 |
| work_keys_str_mv | AT katesmorris thebiochemistryofarchaeaarchaebacteria |