Bacterial Physiology and Metabolism

Cover......Page 1
Half-title......Page 3
Title......Page 5
Copyright......Page 6
Dedication......Page 7
Contents in brief......Page 9
Contents......Page 11
Preface......Page 23
1 Introduction to bacterial physiology and metabolism......Page 25
Ecology......Page 28
Genomics......Page 29
New areas......Page 30
2.1 Elemental composition......Page 31
2.2.1 Five major elements......Page 32
2.2.2 Oxygen......Page 33
2.3.1 Flagella and pili......Page 34
2.3.2 Capsules and slime layers......Page 36
2.3.3.2 Outer membrane......Page 37
2.3.3.3 Cell wall and periplasm......Page 41
2.3.4.1 Properties and functions......Page 45
2.3.4.2 Membrane structure......Page 46
2.3.4.3 Phospholipids......Page 47
2.3.4.4 Proteins......Page 50
2.3.5 Cytoplasm......Page 51
2.3.6 Resting cells......Page 53
S-layer and other surface structures......Page 54
Cell wall......Page 55
Cytoplasmic membrane......Page 56
Cytoplasm......Page 57
Resting cells......Page 58
3.1 Ionophores: models of carrier proteins......Page 59
3.3 Active transport and role of electrochemical gradients......Page 61
3.4 ATP-dependent transport: ATP-binding cassette (ABC) pathway......Page 62
3.5 Group translocation......Page 63
3.6 Precursor/product antiport......Page 64
3.7 Ferric ion (Fe(III)) uptake......Page 65
3.8.1.1 General secretory pathway (GSP)......Page 67
3.8.1.2 Twin-arginine translocation (TAT) pathway......Page 69
3.8.2 Protein translocation across the outer membrane in Gram-negative bacteria......Page 70
3.8.2.3 Type II pathway......Page 71
3.8.2.4 Type III pathway......Page 73
3.8.2.5 Type IV pathway......Page 74
3.8.2.6 Type V pathway: autotransporter and proteins requiring single accessory factors......Page 75
General subjects in transport......Page 76
Active transport......Page 77
ATP-binding cassette (ABC) pathway......Page 78
Protein translocation through general secretion pathway (GSP)......Page 79
Twin-arginine translocation (TAT) pathway......Page 80
Protein translocation in Gram-negative bacteria......Page 81
4 Glycolysis......Page 84
4.1.1 Phosphofructokinase (PFK): key enzyme of the EMP pathway......Page 85
4.1.2 ATP synthesis and production of pyruvate......Page 87
4.1.3.1 Methylglyoxal bypass......Page 88
4.1.3.2 Modified EMP pathways in archaea......Page 89
4.1.4.1 Regulation of phosphofructokinase......Page 90
4.2.1 PEP synthesis......Page 91
4.2.3 Gluconeogenesis in archaea......Page 92
4.3.1 HMP pathway in three steps......Page 93
4.3.2 Additional functions of the HMP pathway......Page 94
4.3.4 F420-dependent glucose-6-phosphate dehydrogenase......Page 95
4.4.3.1 Extracellular oxidation of glucose by Gram-negative bacteria......Page 96
4.5 Phosphoketolase pathways......Page 98
4.5.1 Glucose fermentation by Leuconostoc mesenteroides......Page 99
4.5.2 Bifidum pathway......Page 101
4.6 Use of radiorespirometry to determine glycolytic pathways......Page 102
EMP and modified pathways......Page 104
Methylglyoxal bypass......Page 105
HMP pathway......Page 106
PK pathways......Page 107
Metabolic analysis......Page 108
5.1 Oxidative decarboxylation of pyruvate......Page 109
5.2 Tricarboxylic acid (TCA) cycle......Page 110
5.2.1 Citrate synthesis and the TCA cycle......Page 111
5.3.1 Anaplerotic sequence......Page 112
5.3.2 Glyoxylate cycle......Page 113
5.3.2.1 Regulation of the glyoxylate cycle......Page 114
5.4.1 Incomplete TCA fork......Page 115
5.4.2 Reductive TCA cycle......Page 116
5.5.1 Free energy organic and inorganic electron......Page 117
5.5.1.2 G from the equilibrium constant......Page 118
5.5.2.1 Oxidation/reduction potential......Page 119
5.5.2.2 Free energy from…......Page 120
5.5.4 Sum of free energy change in a series of reactions......Page 121
5.6 Role of ATP in the biological energy transduction process......Page 122
5.6.1 High energy phosphate bonds......Page 123
5.6.2 Adenylate energy charge......Page 124
5.6.4 Interconversion of ATP and the proton motive force (Dp)......Page 125
5.7.1 Proton gradient and membrane potential......Page 126
5.7.3 Proton motive force in acidophiles......Page 127
5.7.4 Proton motive force and sodium motive force in alkalophiles......Page 128
5.8.2.1 Mitochondrial electron transport chain......Page 129
5.8.2.2 Electron carriers......Page 131
5.8.2.3 Diversity of electron transport chains in prokaryotes......Page 132
5.8.2.5 Transhydrogenase......Page 134
5.8.3.1 Q-cycle and Q-loop......Page 135
5.8.4.1 ATP synthase......Page 136
5.8.4.2 Hþ/O ratio......Page 137
5.8.5 Uncouplers......Page 138
5.8.6.2 Naþ-dependent decarboxylase......Page 139
5.9.1 Bacterial bioluminescence......Page 140
5.9.2 Electricity as an energy source in microbes......Page 141
TCA cycle......Page 142
Anaplerotic sequence......Page 143
Adenosine triphosphate (ATP) and ATPase......Page 144
Proton (sodium) motive force, and acid and alkali tolerance......Page 145
Electron transport phosphorylation......Page 147
Other prokaryotic energy transduction......Page 149
6.1 Molecular composition of bacterial cells......Page 150
6.2 Assimilation of inorganic nitrogen......Page 151
6.2.1.1 N2-fixing organisms......Page 152
6.2.1.2 Biochemistry of N2 fixation......Page 153
6.2.1.4 Molecular oxygen and N2 fixation......Page 156
6.2.1.5 Regulation of N2 fixation......Page 158
6.2.2 Nitrate reduction......Page 159
6.2.3 Ammonia assimilation......Page 161
6.3 Sulfate assimilation......Page 163
6.4.1 The pyruvate and oxaloacetate families......Page 164
6.4.4 Aromatic amino acids......Page 165
6.5.1 Salvage pathway......Page 169
6.5.2 Pyrimidine nucleotide biosynthesis through a de novo pathway......Page 172
6.5.4 Synthesis of deoxynucleotides......Page 173
6.6.1 Fatty acid biosynthesis......Page 176
6.6.1.1 Saturated acyl-ACP......Page 177
6.6.1.3 Unsaturated acyl-ACP......Page 178
6.6.2 Phospholipid biosynthesis......Page 180
6.7 Heme biosynthesis......Page 183
6.8.1 Hexose phosphate and UDP-sugar......Page 185
6.8.2 Monomers of murein......Page 187
6.8.4 Precursor of lipopolysaccharide, O-antigen......Page 188
6.9.1 Glycogen synthesis......Page 189
6.9.2.3 Teichoic acid synthesis......Page 191
6.9.3.2 Lipopolysaccharide (LPS) translocation......Page 193
6.10.1 DNA replication......Page 194
6.10.1.1 RNA primer......Page 195
6.10.1.3 DNA polymerase......Page 196
6.10.4 Chromosome segregation......Page 197
6.11.2 Post-transcriptional processing......Page 198
6.12 Translation......Page 199
6.12.2 Synthesis of peptide: initiation, elongation and termination......Page 200
6.12.2.2 Initiation and elongation......Page 201
6.12.3 Post-translational modification and protein folding......Page 202
6.13.1 Flagella......Page 205
6.14 Growth......Page 206
6.14.1.1 Binary fission......Page 207
6.14.1.2 Multiple intracellular offspring......Page 208
6.14.1.3 Multiple offspring by multiple fission......Page 209
6.14.2 Growth yield......Page 211
and maintenance energy......Page 213
6.14.5 Maintenance energy......Page 216
Assimilation of inorganic nitrogen and sulfur......Page 217
Monomer synthesis – others......Page 218
Replication......Page 219
Translation and protein folding......Page 220
Assembly of cellular structures and growth......Page 222
7.1.1 Starch hydrolysis......Page 226
7.1.2 Cellulose hydrolysis......Page 227
7.1.3 Other polysaccharide hydrolases......Page 228
7.1.4 Disaccharide phosphorylases......Page 229
7.2.1 Hexose utilization......Page 230
7.2.2 Pentose utilization......Page 231
7.3.1 Fatty acid utilization......Page 232
7.4 Utilization of alcohols and ketones......Page 237
7.5 Amino acid utilization......Page 238
7.5.3 Amino acid dehydratase......Page 239
7.5.4 Deamination of cysteine and methionine......Page 240
7.5.5 Deamination products of amino acids......Page 241
7.6 Degradation of nucleic acid bases......Page 244
7.7 Oxidation of aliphatic hydrocarbons......Page 247
7.8.1 Oxidation of aromatic amino acids......Page 249
7.8.2 Ortho and meta cleavage, and the gentisate pathway......Page 251
7.9.1 Methanotrophy and methylotrophy......Page 253
7.9.2.1 Characteristics of methanotrophs......Page 254
7.9.2.2 Dissimilation of methane by methanotrophs......Page 257
7.9.3.1 Ribulose monophosphate (RMP) pathway......Page 259
7.9.3.2 Serine–isocitrate lyase (SIL) pathway......Page 260
7.9.3.3 Xylulose monophosphate (XMP) pathway......Page 264
7.10.1 Acetic acid bacteria......Page 265
7.10.2 Acetoin and butanediol......Page 266
7.10.3 Other products of aerobic metabolism......Page 267
Depolymerization of polymers......Page 268
Organic acid utilization......Page 269
Alcohol utilization......Page 270
Amino acid and nucleic acid base utilization......Page 271
Hydrocarbon utilization......Page 272
Methyltrophy......Page 273
Other metabolisms......Page 274
8.1.2 Hydrogen in fermentation......Page 276
8.2 Molecular oxygen and anaerobes......Page 277
8.3 Ethanol fermentation......Page 279
8.4.2 Heterolactate fermentation......Page 281
8.4.3 Biosynthesis in latic acid bacteria (LAB)......Page 283
8.4.6 LAB in fermented food......Page 284
8.5.1.1 Phosphoroclastic reaction......Page 287
8.5.1.2 Butyrate formation......Page 288
8.5.1.3 Lactate fermentation by Clostridium butyricum......Page 289
8.5.1.5 Non-butyrate clostridial fermentation......Page 292
8.5.2 Acetone–butanol–ethanol fermentation......Page 293
8.5.3 Fermentation balance......Page 295
8.6.1 Mixed acid fermentation......Page 296
8.6.2 Butanediol fermentation......Page 297
8.6.3 Citrate fermentation by facultative anaerobes......Page 299
8.6.4 Anaerobic enzymes......Page 301
8.7.1 Succinate–propionate pathway......Page 302
8.7.2 Acrylate pathway......Page 304
8.8.1 Fermentation of individual amino acids......Page 305
8.8.2 Stickland reaction......Page 310
8.10 Hyperthermophilic archaeal fermentation......Page 311
8.11 Degradation of xenobiotics under fermentative conditions......Page 313
Oxygen toxicity......Page 314
Lactic acid......Page 316
Butyrate and butanol......Page 317
Mixed acid fermentation......Page 319
Propionate......Page 320
Fermentation of dicarboxylic acids......Page 321
9 Anaerobic respiration......Page 322
9.1.1 Biochemistry of denitrification......Page 323
9.1.1.1 Nitrate reductase......Page 324
9.1.2 ATP synthesis in denitrification......Page 326
9.1.3 Regulation of denitrification......Page 327
9.1.4 Denitrifiers other than facultatively anaerobic chemoorganotrophs......Page 328
9.2.1 Fe(III) and Mn(IV) reduction......Page 330
9.2.3 Metal reduction and the environment......Page 333
9.3 Sulfidogenesis......Page 334
9.3.1.1 Reduction of sulfate and sulfur......Page 336
9.3.1.2 Carbon metabolism......Page 337
9.3.2.1 Incomplete oxidizers......Page 341
9.3.3 Carbon skeleton supply in sulfidogens......Page 342
9.4.1.1 Hydrogenotrophic methanogens......Page 344
9.4.2 Coenzymes in methanogens......Page 346
9.4.3.1 Hydrogenotrophic methanogenesis......Page 348
9.4.3.2 Methylotrophic methanogenesis......Page 349
9.4.3.3 Aceticlastic methanogenesis......Page 350
9.4.4 Energy conservation in methanogenesis......Page 351
9.4.5 Biosynthesis in methanogens......Page 352
9.5.2.1 Sugar metabolism......Page 354
9.5.2.2 Synthesis of carbon skeletons for biosynthesis in homoacetogens......Page 357
9.6 Dehalorespiration......Page 358
9.6.1 Dehalorespiratory organisms......Page 359
9.7 Miscellaneous electron acceptors......Page 360
9.8.1 Syntrophic bacteria......Page 361
9.8.2 Carbon metabolism in syntrophic bacteria......Page 363
9.9 Element cycling under anaerobic conditions......Page 364
9.9.1 Oxidation of aromatic hydrocarbons under anaerobic conditions......Page 365
9.9.2 Transformation of xenobiotics under anaerobic conditions......Page 367
Denitrification......Page 369
Metal reduction......Page 370
Sulfidogenesis......Page 371
Methanogenesis......Page 372
Homoacetogenesis......Page 373
Anaerobic respiration on miscellaneous electron acceptors......Page 374
Syntrophic associations......Page 375
Degradation of xenobiotics under anaerobic conditions......Page 376
10.1 Reverse electron transport......Page 378
10.2 Nitrification......Page 379
10.2.1 Ammonia oxidation......Page 380
10.2.2 Nitrite oxidation......Page 381
10.3.1 Sulfur bacteria......Page 382
10.3.2 Biochemistry of sulfur compound oxidation......Page 384
10.4 Iron bacteria: ferrous iron oxidation......Page 386
10.5.2 Hydrogenase......Page 388
10.5.3 Anaerobic H2-oxidizers......Page 389
10.6 Carbon monoxide oxidation: carboxydobacteria......Page 390
10.7 Chemolithotrophs using other electron donors......Page 391
10.8.1 Calvin cycle......Page 392
10.8.1.1 Key enzymes of the Calvin cycle......Page 394
10.8.1.2 Photorespiration......Page 396
10.8.2 Reductive TCA cycle......Page 397
10.8.3 Anaerobic CO2 fixation through the acetyl-CoA pathway......Page 398
10.8.4 CO2 fixation through the 3-hydroxypropionate cycle......Page 399
10.9 Chemolithotrophs: what makes them unable to use organics?......Page 401
Nitrification......Page 403
Colourless sulfur bacteria......Page 404
Ferrous iron and other metal oxides......Page 405
Hydrogen oxidizers and carboxydobacteria......Page 406
CO2 fixation......Page 407
11.1 Photosynthetic microorganisms......Page 410
11.1.2 Anaerobic photosynthetic bacteria......Page 411
11.1.3 Aerobic anoxygenic phototrophic bacteria......Page 412
11.2 Photosynthetic pigments......Page 413
11.2.2 Carotenoids......Page 414
11.2.4 Pheophytin......Page 416
11.2.5 Absorption spectra of photosynthetic cells......Page 417
11.3.1 Thylakoids of cyanobacteria......Page 418
11.3.4 Heliobacteria and aerobic anoxygenic phototrophic bacteria......Page 419
11.4 Light reactions......Page 420
11.4.2 Excitation of antenna molecules and resonance transfer......Page 421
11.4.3.2 Green sulfur bacteria......Page 422
11.4.3.3 Purple bacteria......Page 424
11.5.1 CO2 fixation......Page 425
11.5.2.1 Purple bacteria, heliobacteria and aerobic anoxygenic photosynthetic bacteria......Page 426
11.6 Photophosphorylation in halophilic archaea......Page 427
Photosynthetic bacteria......Page 429
Light reactions......Page 430
Photophosphorylation......Page 431
12.1 Mechanisms regulating enzyme synthesis......Page 432
12.1.1 Regulation of transcription by promoter structure and sigma (ó) factor activity......Page 433
12.1.2.1 Inducible and constitutive enzymes......Page 435
12.1.2.2 Enzyme induction......Page 436
12.1.3 Catabolite repression......Page 437
12.1.3.1 Carbon catabolite repression by the cAMP–CRP complex......Page 438
12.1.3.2 Catabolite repressor/activator......Page 439
12.1.3.3 Carbon catabolite repression in Gram-positive bacteria with a low GþC content bacteria with a low GþC content......Page 441
12.1.4.1 Repression......Page 443
12.1.4.2 Attenuation......Page 444
12.1.5 Regulation of gene expression by multiple end products......Page 447
12.1.6.1 Termination and antitermination aided by protein......Page 448
12.1.6.2 Termination and antitermination aided by tRNA......Page 450
12.1.8 Autogenous regulation......Page 452
12.1.9.1 RNA stability......Page 454
12.1.9.3 Modulation of translation and stability of mRNA by protein......Page 455
12.1.9.4 Modulation of translation and stability of mRNA by small RNA and small RNA–protein complex: riboregulation......Page 457
12.2 Global regulation: responses to environmental stress......Page 459
12.2.1 Stringent response......Page 461
12.2.2 Response to ammonia limitation......Page 463
12.2.3 Response to phosphate limitation: the pho system......Page 465
12.2.4 Regulation by molecular oxygen in facultative anaerobes......Page 466
12.2.4.1 arc system......Page 467
12.2.4.2 fnr system......Page 468
12.2.4.3 RegB/RegA system in purple non-sulfur photosynthetic bacteria......Page 469
12.3.1 Feedback inhibition and feedforward activation......Page 483
12.3.2 Enzyme activity modulation through structural changes......Page 484
12.3.2.2 Adenylylation......Page 485
12.3.2.3 Acetylation......Page 486
12.3.2.5 Regulation through physical modification and dissociation/association......Page 487
12.4.2 Regulatory network......Page 488
12.5 Secondary metabolites......Page 490
12.6.2 Fermentative amino acid production......Page 491
Promoter and ó-factor......Page 492
Termination/antitermination......Page 493
Two-component systems......Page 494
Post-transcriptional regulation......Page 495
Stringent response......Page 496
Nitrogen control......Page 497
Quorum sensing......Page 498
Pho system......Page 499
Heat shock......Page 500
Cold shock......Page 501
Oxidative stress......Page 502
Chemotaxis......Page 503
Adaptive mutation......Page 504
Enzyme activity modulation and metabolic flux......Page 505
13.1 Survival and energy......Page 506
13.2.1 Carbohydrate reserve materials: glycogen and trehalose......Page 507
13.2.2 Lipid reserve materials......Page 508
13.2.2.1 Poly-Beta -hydroxyalkanoate (PHA)......Page 509
13.2.2.3 Wax ester and hydrocarbons......Page 510
13.2.3 Polypeptides as reserve materials......Page 511
13.2.4 Polyphosphate......Page 512
13.3 Resting cells......Page 513
13.3.3 Viable but non-culturable (VBNC) cells......Page 514
13.3.5 Programmed cell death (PCD) in bacteria......Page 516
Survival and energy......Page 517
Resting cells......Page 518
Index......Page 520