Cohen Microbial Biochemistry

2. Auflage 2011
ISBN: 978-90-481-9437-7
Verlag: Springer Netherland
Format: PDF
Kopierschutz: 1 - PDF Watermark

E-Book, Englisch, 558 Seiten, eBook

Reihe: Biomedical and Life Sciences (R0)

Microbial physiology, biochemistry, and genetics allowed the formulation of concepts that turned out to be important in the study of higher organisms. In the first section, the principles of bacterial growth are given, as well as the description of the different layers that enclose the bacterial cytoplasm, and their role in obtaining nutrients from the outside media through different permeability mechanism described in detail. A chapter is devoted to allostery and is indispensable for the comprehension of many regulatory mechanisms described throughout the book. Another section analyses the mechanisms by which cells obtain the energy necessary for their growth, glycolysis, the pentose phosphate pathway, the tricarboxylic and the anaplerotic cycles. Two chapters are devoted to classes of microorganisms rarely dealt with in textbooks, namely the Archaea, mainly the methanogenic bacteria, and the methylotrophs. Eight chapters describe the principles of the regulations at the transcriptional level, with the necessary knowledge of the machineries of transcription and translation. The next fifteen chapters deal with the biosynthesis of the cell building blocks, amino acids, purine and pyrimidine nucleotides and deoxynucleotides, water-soluble vitamins and coenzymes, isoprene and tetrapyrrole derivatives and vitamin B12. The two last chapters are devoted to the study of protein-DNA interactions and to the evolution of biosynthetic pathways. The considerable advances made in the last thirty years in the field by the introduction of gene cloning and sequencing and by the exponential development of physical methods such as X-ray crystallography or nuclear magnetic resonance have helped presenting metabolism under a multidisciplinary attractive angle. The level of readership presupposes some knowledge of chemistry and genetics at the undergraduate level. The target group is graduate students, researchers in academia and industry.

Zielgruppe

Research

Autoren/Hrsg.

Cohen, G.N.

Inhaltsverzeichnis

1;Foreword;6
2;Contents;8
3;Abbreviations;22
4;Introduction;28
5;Chapter 1: Bacterial Growth;30
5.1;The Lag Phase;30
5.2;The Exponential Phase;30
5.3;Linear Growth;31
5.4;The Yield of Growth;32
5.5;Variation of the Growth Rate at Limiting Carbon Source Concentrations;33
5.6;Continuous Growth: The Chemostat;34
5.7;Advantages of the Continuous Exponential Culture;36
5.8;Diauxic Growth;36
5.9;Selected References;39
5.9.1;Bacterial Growth: Diauxie;39
5.9.2;Linear Growth;39
5.9.3;Continuous Growth: The Chemostat;39
5.9.4;Influence of Growth Rate on Cellular Constituents;39
5.9.5;Adaptive (Inducible) Enzymes: Prehistory;39
6;Chapter 2: The Outer Membrane of Gram-negative Bacteria and the Cytoplasmic Membrane;40
6.1;The Outer Membrane of Gram-Negative Bacteria;40
6.2;The Cytoplasmic Membrane;41
6.3;Energy Generation;42
6.3.1;ATP Synthase;42
6.4;Subunit Composition of the ATP Synthase;43
6.5;ATP Synthesis in Archaea;45
6.6;Selected References;45
6.6.1;ATP Synthase;45
7;Chapter 3: Peptidoglycan Synthesis and Cell Division;46
7.1;General Structure;46
7.2;Assembly of the Peptidoglycan Unit;47
7.3;The Membrane Steps;48
7.4;Assembly of the Murein Sacculus;49
7.5;Penicillin Sensitivity;49
7.6;Cell Division;50
7.7;Selected References;51
7.7.1;Cell Division;51
8;Chapter 4: Cellular Permeability;52
8.1;Accumulation, Crypticity, and Selective Permeability;53
8.2;beta-Galactoside Permease;54
8.2.1;Accumulation in Induced Cells: Kinetics and Specificity;55
8.2.2;The Induced Synthesis of Galactoside Permease;58
8.2.3;Functional Significance of Galactoside Permease: Specific Crypticity;59
8.2.4;Functional Relationships of Permease: Induction;61
8.2.5;Genetic Relationships of Galactosidase and Galactoside Permease;61
8.2.6;Galactoside Permease as Protein;62
8.3;Periplasmic Binding Proteins and ATP Binding Cassettes;65
8.4;Phosphotransferases: The PTS System;68
8.5;TRAP Transporters;70
8.6;A Few Well-identified Cases of Specific Cellular Permeability;71
8.6.1;Amino Acid Permeases;71
8.6.2;Peptide Permeases;72
8.7;Porins;74
8.8;Iron Uptake;76
8.9;Conclusion;77
8.10;Selected References;77
8.10.1;beta-Galactoside Permease;77
8.10.2;Amino Acid Permeases;77
8.10.3;Periplasmic Proteins and ATP-Binding Cassettes;77
8.10.4;Phosphotransferase System;78
8.10.5;Peptide Permeaes;78
8.10.6;TRAP Transporters;78
8.10.7;Porins;78
9;Chapter 5: Allosteric Enzymes;79
9.1;Allosteric Inhibition and Activation;82
9.2;An Alternative Model;89
9.3;Conclusion;90
9.4;Selected References;90
10;Chapter 6: Glycolysis, Gluconeogenesis and Glycogen Synthesis;91
10.1;Glycogen Degradation;91
10.2;Glycolysis;91
10.2.1;Hexokinase;93
10.2.2;Glucose 6-Phosphate Isomerase;93
10.2.3;Phosphofructokinase;94
10.2.3.1;A Second Phosphorylation Follows the Isomerization Step;94
10.2.3.2;Regulation of Phosphofructokinase in Bacteria;95
10.2.4;Fructose 1,6-Bisphosphate Aldolase;96
10.2.5;Triose Phosphate Isomerase;96
10.2.5.1;As for the Preceding Enzyme, This One Is not Subject to Metabolic Regulation;96
10.2.6;Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH);96
10.2.7;Phosphoglycerate Kinase;97
10.2.8;Phosphoglyceromutase;97
10.2.9;Enolase;97
10.2.10;Pyruvate Kinase;98
10.3;Gluconeogenesis;98
10.4;Fructose Bisphosphatase in Microorganisms;98
10.5;Glycogen Synthesis;99
10.5.1;Glycogen Synthase;99
10.6;Control of Glycogen Biosynthesis;100
10.7;Branching Enzyme;100
11;Chapter 7: The Pentose Phosphate and Entner-Doudoroff Pathways;101
11.1;The Pentose Phosphate Pathway;101
11.2;The Enzymes of the Oxidative Phase;101
11.2.1;Glucose 6-Phosphate Dehydrogenase;101
11.2.2;6-Phosphogluconolactonase;102
11.2.3;6-Phosphogluconate Dehydrogenase (Decarboxylating);102
11.2.4;Ribose Phosphate Isomerase;102
11.3;The Enzymes of the Non-oxidative Phase;102
11.3.1;Transketolase;103
11.3.2;Transaldolase;104
11.3.3;Ribulose-5-Phosphate-3-Epimerase;104
11.4;Regulation of the Pentose Phosphate Pathway;105
11.4.1;The Entner-Doudoroff Pathway;105
12;Chapter 8: The Tricarboxylic Acid Cycle and the Glyoxylate Bypass;106
12.1;The origin of acetyl CoA: The Pyruvate Dehydrogenase Complex;106
12.2;Overview of the Tricarboxylic Acid (TCA) Cycle;108
12.2.1;Origin of the Oxaloacetate;108
12.3;Organization of the Enzymes of the Tricarboxylic Acid Cycle;123
12.4;The Tricarboxylic Acid Cycle Is a Source of Biosynthetic Precursors;124
12.5;The Anaplerotic Glyoxylic Pathway Bypass;124
13;Chapter 9: ATP-Generating Processes: Respiration and Fermentation;127
13.1;Respiration;127
13.2;Fermentation;130
13.3;Acetone-Butanol Fermentation;130
13.4;The Stickland Reaction;131
13.5;Ornithine Fermentation;131
13.6;Glycine and Proline Degradation;132
13.7;Threonine Degradation;132
13.8;Glutamate Degradation;133
13.9;Lysine Degradation;134
13.10;Arginine Fermentation;135
13.11;Methionine Degradation;136
13.12;D-Selenocystine and D-Cysteine Degradation;136
13.13;Selected References;137
13.13.1;NADH-Ubiquinone Oxidoreductases;137
13.13.2;Erom Quinones to Oxygen;137
13.13.3;The Stickland Reaction;137
13.13.4;Arginîne and Ornithine Degradation;137
13.13.5;Threonine Degradation;138
13.13.6;Glycine Degradation;138
13.13.7;Proline Degradation;138
13.13.8;Glutamate Degradation;138
13.13.9;Lysine Degradation;138
13.13.10;Methionine gamma-Lyase;138
13.13.11;D-Selenocystine and D-Cysteine Degradation;139
14;Chapter 10: Biosynthesis of Lipids;140
14.1;Biosynthesis of Short Chain Fatty Acids;140
14.2;Biosynthesis of Long-Chain Fatty Acids;141
14.2.1;Synthesis of Acetyl CoA;141
14.2.2;Synthesis of Malonyl CoA;141
14.2.3;From Malonyl CoA to Palmitate;142
14.3;Regulation of Yeast Fatty Acid Synthesis at the Genetic Level;145
14.4;Regulation of Fatty Acid Synthesis in Bacteria;147
14.5;Biosynthesis of Triglycerides;147
14.6;Biosynthesis of Phosphoglycerides;147
14.7;Cyclopropane Fatty Acid Synthase (CFA Synthase);148
14.8;Selected References;150
14.8.1;Short Chain Fatty Acid Synthesis;150
14.8.2;Fatty Acid Synthesis and Its Regulation;150
14.8.3;Cyclopropane Fatty Acid Synthetase;150
15;Chapter 11: Iron-Sulfur Proteins;151
15.1;Iron-Sulfur Clusters;151
15.2;2Fe-2S Clusters;152
15.3;4Fe-4S Clusters;152
15.4;3Fe-4S Clusters;153
15.5;Other Fe-S Clusters;153
15.6;Biosynthesis of Fe-S Clusters;153
15.7;Iron-Sulfur Proteins;154
15.8;Selected References;156
16;Chapter 12: The Archaea;157
16.1;Chemical Characteristics of Archaea;159
16.2;Archaea: Fossil Record;160
16.3;Economic Importance of the Archaea;161
16.4;Selected References;161
17;Chapter 13: Methanogens and Methylotrophs;162
17.1;Methanogens and Methanogenesis;163
17.1.1;Reduction of CO2;163
17.1.2;Formylmethanofuran Dehydrogenase;165
17.1.3;Formylmethanofuran: Tetrahydromethanopterin Formyltransferase;166
17.1.4;Methenyltetrahydromethanopterin Cyclohydrolase;167
17.1.5;5, 10-Methylenetetrahydromethanopterin Dehydrogenase;167
17.1.6;5, 10-Methylenetetrahydromethanopterin F420 Oxidoreductase;168
17.1.7;The Methylreductase: Methyl Coenzyme M Reductase;168
17.1.8;Simplification of the Methylreductase System;170
17.1.9;Structure of the Methylreductase;171
17.1.10;Source of the Energy Needed for the Growth of Methanogens;172
17.1.11;Biosynthesis of Some Cofactors Involved in Methanogenesis;172
17.1.12;Methanofuran;172
17.1.13;Methanopterin;172
17.1.14;Coenzyme M;173
17.1.15;7-Mercaptoheptanoylthreoninephosphate (Coenzyme B);174
17.1.16;Biosynthesis of Coenzyme F420;175
17.1.17;Biosynthesis of Factor F430;175
17.1.18;Biosynthesis of Factor III;176
17.2;Methylotrophs;176
17.2.1;Methanotrophs;176
17.2.2;Metabolism of Methyl Compounds;177
17.2.3;Methanol Dehydrogenase (MDH);178
17.2.4;Anaerobic Oxidation of Methane;178
17.2.5;Methylamine Dehydrogenase;179
17.2.6;Carbon Assimilation by Methylotrophs;179
17.3;Carboxydotrophs;181
17.4;Selected References;183
17.4.1;Methanogenesis;183
17.4.2;Biosynthesis of the Methanogenic Cofactors;183
17.4.3;Biosynthesis of Methanofuran;183
17.4.4;Biosynthesis of Methanopterin;183
17.4.5;Biosynthesis of Coenzyme M;183
17.4.6;Biosynthesis of 7-Mercaptoheptanoylthreoninephosphate (Coenzyme B);183
17.4.7;Biosynthesis of Coenzyme F420;184
17.4.8;Biosynthesis of Factor F430;184
17.4.9;Anaerobic Oxidation of Methane;184
17.4.10;Carboxydotrophs;184
18;Chapter 14: Enzyme Induction in Catabolic Systems;185
18.1;The Specificity of Induction;185
18.2;De Novo Synthesis of beta-Galactosidase;186
18.3;Constitutive Mutants;188
18.4;Pleiotropy of the Constitutive Mutants;189
18.5;The Genetic Control and the Cytoplasmic Expression of Inducibility in the Synthesis of beta-Galactosidase in E. coli. The Lac R;190
18.6;Operators and Operons;196
18.7;Selected References;199
18.7.1;Specificity of Induction. De Novo Synthesis;199
18.7.2;Pleiotropy of the i Gene;199
18.7.3;Thiogalactoside Transacetylase;199
18.7.4;Genetics;199
18.7.5;Repressors and Operators;199
19;Chapter 15: Transcription: RNA Polymerase;200
19.1;The Synthesis of Messenger RNA: The Bacterial RNA Polymerase;201
19.2;Termination of Transcription in Prokaryotes;204
19.2.1;Yeast RNA Polymerases;205
19.2.2;Archaeal RNA Polymerases;206
19.3;Transcription Termination and PolyA Tails;207
19.4;Selected References;207
19.4.1;Trans-acting Transcription Factors;207
19.4.2;Eukaryotic RNA Polymerases;207
19.4.3;Termination of Transcription;208
20;Chapter 16: Negative Regulation;209
20.1;Induction Is Correlated with the Synthesis of a Specific Messenger;209
20.2;Isolation of the Lac Repressor;211
20.3;The lac Operator Is a DNA sequence;213
20.4;Direct Observation of Transcription Factor Dynamics in a Living Cell;219
20.5;Selected References;219
20.5.1;Messenger RNA;219
20.5.2;Isolation of Lac Repressor and lac Operator;220
20.5.3;Operators 02 and 03;220
20.5.4;Formation of Loop Structures in DNA;220
20.5.5;Quantifying lac Repressor Kinetics;220
21;Chapter 17: Enzyme Repression in Anabolic Pathways;221
21.1;Description of the Phenomenon;221
21.2;Isolation of Derepressed (Constitutive) Mutants in Biosynthetic Pathways. The Use of Structural Analogues;225
21.3;Replacement of Methionine by Selenomethionine in Proteins;226
21.4;Selected References;227
21.4.1;Repression of the Biosynthesis of Anabolic Enzymes;227
21.4.2;Incorporation of Amino Acid Analogs into Proteins;227
22;Chapter 18: Positive Regulation;228
22.1;The Promoter Region;229
22.2;Role of Cyclic AMP and of the CAP Protein in the Binding of RNA Polymerase to the Promoter Region;230
22.3;The Synthesis and Degradation of Cyclic 232
22.4;How Does Glucose Exert Its Inhibitory Effect on E. coli beta-Galactosidase Synthesis?;233
22.5;Selected References;233
22.5.1;Catabolic Repression;233
22.5.2;Effects of Cyclic AMP on the Glucose Effect;234
22.5.3;The Promoter;234
22.5.4;The CAP Protein;234
22.5.5;Mode of Action of Cyclic 234
23;Chapter 19: The Ribosomes;235
23.1;The Components of E. coli Ribosomes;236
23.2;The Ribosomes of Eukaryotes and of Archaea;237
23.3;Mechanistic Aspects of Translation of Messenger RNA to Protein by Ribosomes;238
23.4;Selected References;239
23.4.1;General;239
23.4.2;Eukaryotic Ribosomes;240
23.4.3;Crystallography;240
24;Chapter 20: The Genetic Code, the Transfer RNAs and the Aminoacyl-tRNA-Synthetases;241
24.1;The Genetic Code;241
24.2;The Transfer RNAs;244
24.3;Selected References;249
24.3.1;Colinearity of Genes and Proteins;249
24.3.2;The Genetic Code;249
24.3.3;Selenocysteine and Pyrrolysine;249
24.3.4;Transfer RNAs;249
24.3.5;Aminoacyl-tRNA Synthetases;249
24.3.6;RNA-Dependent Cysteine Biosynthesis in Archaea;249
25;Chapter 21: Attenuation;250
25.1;Regulation of the trp Operon in Bacillus subtilis;254
25.2;General Remarks on Regulatory Mechanisms;254
25.3;Selected References;255
25.3.1;Attenuation;255
25.3.2;TRAP Protein;256
26;Chapter 22: Riboswitches;257
26.1;Mechanisms of Riboswitches;259
26.2;Selected References;260
27;Chapter 23: The Biological Fixation of Nitrogen;261
27.1;Control of Nitrogenase Synthesis and Activity;264
27.2;Selected References;266
27.2.1;General Reviews;266
27.2.2;Fe-Protein;266
27.2.3;Mo-Fe Protein;266
27.2.4;Fe-MoCo;266
27.2.5;Oxygen Relations of Nitrogen Fixation in Cyanobacteria;266
28;Chapter 24: How Biosynthetic Pathways have been Established;267
28.1;Use of Isotopes;267
28.2;Use of Auxotrophic Mutants;270
28.3;Enzymatic Analysis;272
28.4;Selected References;272
28.4.1;Isotopic Competition;272
28.4.2;Isolation of Auxotrophic Mutants;272
29;Chapter 25: The Aspartic Acid Family of Amino Acids: Biosynthesis;273
29.1;The Biosynthesis of Aspartic Acid and Asparagine;273
29.2;Biosynthesis of Lysine from Aspartate Semialdehyde in Bacteria;276
29.3;The Synthesis of Dipicolinic Acid, a Substance Present in the Spores of Gram-Positive Bacilli;278
29.4;The Reduction of Aspartate Semialdehyde to Homoserine, the Common Precursor of Methionine and Threonine;279
29.5;Biosynthesis of Methionine from Homoserine;279
29.6;S-Adenosylmethionine (SAM) Biosynthesis;284
29.7;Biosynthesis of Threonine from Homoserine;285
29.8;Biosynthetic Threonine Dehydratase;286
29.9;Isoleucine Biosynthesis;287
29.10;Summary of the Biosynthetic Pathway of the Aspartate Family of Amino Acids;288
29.10.1;Ectoine Biosynthesis;289
29.11;Selected References;289
29.11.1;Asparagine;290
29.11.2;Threonine Synthase;290
29.11.3;Diaminopimelate Decarboxylase;290
29.11.4;Methionine Biosynthesis; Direct Sulfhydrylation Pathway;290
30;Chapter 26: Regulation of the Biosynthesis of the Amino Acids of the Aspartic Acid Family in Enterobacteriacea;291
30.1;A Paradigm of Isofunctional and Multifunctional Enzymes and of the Allosteric Equilibrium;291
30.1.1;Two Aspartokinases in E. coli;292
30.1.2;The Threonine-Sensitive Homoserine Dehydrogenase of E. coli;294
30.1.3;Isolation of a Mutant Lacking the Lysine-Sensitive Aspartokinase and of Revertants Thereof;294
30.1.4;Evidence That the Threonine-Sensitive Aspartokinase and Homoserine Dehydrogenase of E. coli Are Carried by the Same Bifunctiona;297
30.1.5;The Binding of Threonine to Aspartokinase I-Homoserine Dehydrogenase I;297
30.1.6;The Binding of Pyridine Nucleotides to Aspartokinase I-Homoserine Dehydrogenase I;299
30.1.7;The Effects of Threonine on Aspartokinase I-Homoserine Dehydrogenase I Are Not Only Due to Direct Interactions;300
30.1.8;The Allosteric Transition of Aspartokinase I-Dehydrogenase I;302
30.1.9;Aspartokinase II-Homoserine Dehydrogenase II;305
30.1.10;Aspartokinase III;307
30.1.10.1;From Homoserine to Methionine;307
30.1.10.2;From Threonine to Isoleucine;308
30.1.10.3;Multifunctional Proteins;309
30.2;Regulations at the Genetic Level;310
30.2.1;The Threonine Operon;310
30.2.2;Regulation of the Lysine Regulon at the Genetic Level;312
30.2.3;Regulation of Methionine Biosynthesis at the Genetic Level;312
30.2.4;The Methionine Repressor;314
30.2.5;The metR Gene and Its Product;318
30.2.6;The Regulation of Isoleucine Synthesis at the Genetic Level;320
30.2.7;Appendix: More on Regulons;320
30.3;Selected References;321
30.3.1;Isofunctional Aspartokinases;321
30.3.2;Aspartokinases-Homoserine Dehydrogenases I and II. Structure and Regulation of Activity;321
30.3.3;The Threonine Operon and Its Regulation;322
30.3.4;Aspartokinase III. Crystallography;322
30.3.5;Regulation of Methionine Biosynthesis. The Methionine Repressor;322
30.3.6;Regulation of the Synthesis of the Branched-Chain Amino Acids;322
30.3.7;The Leucine-Lrp Regulon;322
31;Chapter 27: Other Patterns of Regulation of the Synthesis of Amino Acids of the Aspartate Family;323
31.1;Concerted Feedback Inhibition of Aspartokinase Activity in Rhodobacter capsulatus (Formerly Rhodopseudomonas capsulata);323
31.2;Pseudomonads;324
31.3;Specific Reversal of a Particular Feedback Inhibition by Other Essential Metabolites. The Case of Rhodospirillum rubrum;326
31.3.1;The Particular Case of Spore-Forming bacilli;327
31.4;Some Other Cases;330
31.5;Conclusion;330
31.6;Selected References;330
31.6.1;Concerted Feedback Inhibition;330
31.6.2;Pseudomonads;331
31.6.3;Rhodospirillum rubrum;331
31.6.4;Spore-Forming bacilli;331
32;Chapter 28: Biosynthesis of the Amino Acids of the Glutamic Acid Family and Its Regulation;332
32.1;The Biosynthesis of Glutamine;332
32.1.1;Biosynthesis of Glutamine: Cumulative Feedback Inhibition;332
32.1.2;Biosynthesis of Glutamine: The Covalent Modification of Glutamine Synthetase;334
32.1.3;Glutamine Synthetase Structure;335
32.1.4;Reversible Adenylylation of the Glutamine Synthetase;338
32.1.5;Regulation of Glutamine Synthetase Activity by Covalent Adenylylation;339
32.1.6;The Regulation of the Synthesis of Glutamine Synthetase also Involves the Two Forms of PII and UTase/UR;340
32.1.7;Glutamine Synthetase in Other Microorganisms;342
32.2;The Biosynthesis of Glutamate;344
32.2.1;Glutamate Dehydrogenase;344
32.2.2;Glutamate Synthase;344
32.3;Biosynthesis of Proline;345
32.3.1;Utilization of Proline;347
32.4;The Biosynthesis of Arginine and Polyamines;348
32.4.1;Biosynthesis of Arginine;348
32.4.2;Regulation of Arginine Biosynthesis at the Transcriptional Level;351
32.4.3;The Arginine Repressor;351
32.4.4;Polyamine Biosynthesis;352
32.4.5;Utilization of Arginine as Sole Nitrogen Source by B. subtilis;355
32.5;Nitric Oxide Synthase in Bacteria;356
32.6;The Biosynthesis of Lysine in Yeasts and Molds;356
32.6.1;The Aminoadipic Acid Pathway;357
32.7;Selected References;360
32.7.1;Glutamine Synthetase Activity and Its Regulation by Covalent Modification: Structure;360
32.7.2;Glutamine Synthetase: Regulation of Gene Expression;360
32.7.3;The Levels of Glutamine Synthetase Are also Regulated by Oxidation Followed by Proteolytic Degradation;360
32.7.4;Glutamate Synthase;360
32.7.5;Proline Biosynthesis;360
32.7.6;Arginine Biosynthesis and Regulation;361
32.7.7;The Arginine Repressor;361
32.7.8;The Methionine Salvage Pathway;361
32.7.9;Nitric Oxide Synthase;361
32.7.10;Aminoadipic Acid Pathway;361
33;Chapter 29: Biosynthesis of Amino Acids Derived from Phosphoglyceric Acid and Pyruvic Acid;362
33.1;Biosynthesis of Glycine and Serine;362
33.1.1;Regulation of Serine Hydroxymethyltransferase at the Transcriptional Level;364
33.2;Biosynthesis of Cysteine;365
33.2.1;O-Acetylation of Serine;367
33.2.2;Cysteine Synthesis in Methanogens;367
33.2.3;Allosteric Regulation of Cysteine Synthesis;368
33.2.4;Regulation of Cysteine Synthesis at the Genetic Level;368
33.3;Biosynthesis of Alanine;369
33.4;Biosynthesis of Valine;370
33.5;Biosynthesis of Leucine;372
33.6;Isoleucine Synthesis from Pyruvate;374
33.7;Regulation of Valine, Isoleucine and Leucine Biosynthesis;374
33.8;Selected References;375
33.8.1;Serine Biosynthesis;375
33.8.2;Serine Hydroxymethylase;376
33.8.3;Sulfite Reductase;376
33.8.4;Cysteine Synthesis in Methanogens;376
33.8.5;Valine and Leucine;376
33.8.6;Isoleucine Synthesis from Pyruvate;376
33.8.7;Aspartate-beta-Decarboxylase;376
34;Chapter 30: Selenocysteine and Selenoproteins;377
34.1;Outlook;377
34.2;Enzymes Containing Selenocysteine;378
34.2.1;Formate Dehydrogenases;378
34.2.2;The Glycine Reductase Complex;378
34.2.3;The Nicotinic Acid Hydroxylase of Clostridium barkeri;379
34.2.4;Hydrogenases;380
34.2.5;Xanthine Dehydrogenase;380
34.2.6;Acetoacetyl CoA Thiolase;381
34.2.7;Gene Products Involved in Selenocysteine Biosynthesis and Incorporation;381
34.2.8;Selenocysteine Synthase;382
34.2.9;Selenophosphate Synthetase;382
34.2.10;Selenocysteine Lyase;382
34.2.11;Selenocysteyl tRNA;382
34.2.12;Insertion Sequences (SECIS Elements);384
34.2.13;Selenocysteine and Archaea;384
34.3;Biochemical Function of the Selenocysteine Residue in Catalysis;385
34.4;Selected References;385
35;Chapter 31: Biosynthesis of Aromatic Amino Acids and Its Regulation;386
35.1;The Common Pathway (Shikimic Pathway);386
35.1.1;Formation of Shikimic Acid;386
35.1.2;Formation of Chorismic Acid;390
35.1.3;Physiological Aspects of the Regulation of the Common Pathway;391
35.1.4;Characteristics of the Common Pathway in Several Organisms;392
35.2;Biosynthesis of Phenylalanine and Tyrosine from Chorismic Acid;393
35.2.1;The tyrR Regulon;394
35.2.2;Regulation of the pheA Gene by Attenuation;395
35.2.3;Other Organisms: The Arogenate Pathway of Phenylalanine and Tyrosine Biosynthesis;395
35.2.4;Aspartate as a Presursor of Aromatic Amino Acids;396
35.3;The Biosynthesis of Tryptophan from Chorismic Acid;397
35.3.1;Anthranilate Synthase-Anthranilate Phosphoribosyltransferase;398
35.3.2;Phosphoribosylanthranilate Isomerase-Indoleglycerophosphate Synthase;399
35.3.3;Tryptophan Synthase;400
35.3.4;Regulation of Tryptophan Biosynthesis at the Genetic Level: The Tryptophan Repressor;404
35.3.5;A Unitary Model for Induction and Repression;406
35.3.6;Isolation of the Trp Repressor;406
35.4;Enterochelin (Enterobactin) Biosynthesis;408
35.4.1;The Synthesis of 2,3-Dihydroxybenzoic Acid;408
35.5;Selected References;410
35.5.1;The Common Pathway;410
35.5.2;Biosynthesis of Phenylalanine and Tyrosine;410
35.5.3;DKFP Pathway: Aspartate as a Precursor of Aromatic Amino Acids;410
35.5.4;TyrR;411
35.5.5;Tryptophan Synthesis;411
35.5.6;Tryptophan Repressor: Functional Aspects;411
35.5.7;Enterochelin;411
36;Chapter 32: The Biosynthesis of Histidine and Its Regulation;412
36.1;Regulation of Histidine Biosynthesis at the Genetic Level;415
36.2;Synthesis of Diphthamide, a Modified Histidine, by Archaea;420
36.3;Selected References;421
36.3.1;Histidine Biosynthesis and Its Regulation;421
36.3.2;PR-ATP Pyrophosphorylase;421
36.3.3;Attenuation;421
36.3.4;Diphthamide in Archaea;421
37;Chapter 33: The Biosynthesis of Nucleotides;422
37.1;The Biosynthesis of Pyrimidine Nucleotides;422
37.1.1;Synthesis of 5-Phosphoribosyl-1-Pyrophosphate (PRPP);422
37.1.2;Synthesis of Carbamylphosphate;423
37.1.3;The Synthesis of Cytidine and Uridine Triphosphates;425
37.1.4;Direct Utilization of Pyrimidines and of Their Derivatives;427
37.1.5;Aspartate Transcarbamylase of E. coli;427
37.1.6;The Aspartate Transcarbamylase of Other Organisms;433
37.1.7;Regulation of Pyrimidine Nucleotide Synthesis at the Genetic Level;434
37.2;The Biosynthesis of Purine Nucleotides;435
37.2.1;Biosynthesis of 5-Amino-4-Imidazole Carboxamide Ribonucleotide;435
37.2.2;Synthesis of Inosinic Acid;438
37.2.3;The Synthesis of Guanylic and Adenylic Acids;439
37.2.4;Remarks on the Control of Purine Nucleotide Biosynthesis;440
37.2.5;From Nucleoside Monophosphates to Nucleoside Diphosphates and Triphosphates;442
37.3;Selected References;442
37.3.1;Carbamylphosphate Synthetase;442
37.3.2;PRPP Synthetase;442
37.3.3;Aspartate Transcarbamylase;442
37.3.4;CAD Protein;443
37.3.5;Nucleoside Diphosphokinase;443
37.3.6;PRPP Amidotransferase;443
38;Chapter 34: The Biosynthesis of Deoxyribonucleotides;444
38.1;The Formation of Deoxyribonucleoside Diphosphates from Ribose Nucleoside Diphosphates;444
38.2;The Ribosenucleoside Diphosphate (NDP) Reductase System of E. coli;444
38.2.1;Thioredoxin and Thioredoxin Reductase;444
38.2.2;Ribonucleoside Reductase;447
38.3;Regulation of the Activity of Ribonucleoside Diphosphate Reductase;449
38.4;dCMP Deaminase and Thymidylate Synthase;450
38.5;dUTPase;452
38.6;The Ribonucleoside Phosphate Reductase of Other Organisms;452
38.7;A Ribonucleotide Triphosphate Reductase Reaction in E. coli Grown Under Anaerobic Conditions;453
38.8;The Synthesis of Deoxyribonucleoside Triphosphates from the Diphosphates;454
38.9;Organization of DNA Precursor Synthesis in Eukaryotic Cells;454
38.10;Selected References;455
38.10.1;Thioredoxin and Glutaredoxin;455
38.10.2;Ribonucleoside Diphosphate and Triphosphate Reductases;455
38.10.3;Thymidylate Kinases;455
38.10.4;Nucleoside Diphosphate Kinase;455
39;Chapter 35: Biosynthesis of Some Water-Soluble Vitamins and of Their Coenzyme Forms;456
39.1;Biosynthesis of Thiamin and Cocarboxylase;456
39.2;Control of Thiamin Biosynthesis;458
39.3;Biosynthesis of Riboflavin;460
39.4;Biosynthesis of Nicotinamide, NAD+ and NADP+;462
39.5;Regulation of the Biosynthesis of Nicotinamide and Its Derivatives;465
39.6;NAD+ and the ADP-Ribosylation of Proteins;466
39.7;Biosynthesis of Para-Aminobenzoic Acid, of Folic Acid and Its Derivatives;467
39.8;Biosynthesis of Vitamin B6 Pyridoxine, and of Its Derivatives, Pyridoxal, Pyridoxamine and Pyridoxal Phosphate;470
39.9;Biosynthesis of Biotin, Biotin CO2, and Biocytin;472
39.10;The Biotin Operon and Its Repressor;475
39.11;Biosynthesis of Lipoic Acid;476
39.12;Biosynthesis of Pantothenate and Coenzyme A;477
39.12.1;The Synthesis of Pantothenic Acid;477
39.12.2; The Synthesis of Coenzyme A from Pantothenic Acid;479
39.12.3; The Acyl Carrier Protein;480
39.13;The Biosynthesis of Inositol;480
39.14;Biosynthesis of Pyrroloquinoline Quinone;480
39.15;Selected References;483
39.15.1;Thiamin;483
39.15.2;Riboflavin;483
39.15.3;Pyridoxal Phosphate;483
40;Chapter 36: Biosynthesis of Carotene, Vitamin A, Sterols, Ubiquinones and Menaquinones;484
40.1;Synthesis of the Common Precursor;484
40.2;The Non-mevalonate Pathway of Isoprenoid Precursor (Dimethylallyl Pyrophosphate) Biosynthesis;486
40.3;Synthesis of beta-Carotene, Carotenoids and Vitamin A;488
40.3.1;Synthesis of the Carotenoids;488
40.3.2;Regulation of Carotenoid Synthesis;491
40.3.3;Synthesis of Vitamin A;492
40.4;Synthesis of Sterols;492
40.5;The Biosynthesis of Ubiquinones and Menaquinones;494
40.6;Selected References;497
40.6.1;Mevalonate and Non-mevalonate Pathways;497
40.6.2;Biosynthesis of Water-Soluble Vitamins;498
40.6.3;Pyridoxine;498
40.6.4;Carotenoids;498
40.6.5;Menaquinones;498
41;Chapter 37: Biosynthesis of the Tetrapyrrole Ring System;499
41.1;Synthesis of Protoporphyrin;499
41.2;Synthesis of Heme from Protoporphyrin;504
41.3;Heme Biosynthesis in Archaea;505
41.4;Synthesis of Chlorophyll from Protoporphyrin;505
41.5;Biosynthesis of the Phycobilin Chromophores. Chromatic Adaptation;508
41.6;A Type of Chromatic Adaptation Under Conditions of Sulfur Starvation;511
41.7;Selected References;512
41.7.1;The Tetrapyrroles;512
41.7.2;ALA Synthesis;512
41.7.3;Heme Biosynthesis in Archaea;512
41.7.4;Phycobilins;512
41.7.5;Complementary Chromatic Adaptation;513
41.7.6;The Effect of Sulfur Starvation on Chromatic Adaptation;513
42;Chapter 38: Biosynthesis of Cobalamins Including Vitamin B12;514
42.1;Cobinamide Biosynthesis;518
42.2;From GDP-Cobinamide to Cobalamin;520
42.3;Selected References;521
42.3.1;Threonine Kinase and the Origin of the Aminopropanol Residue;521
42.3.2;Origin of the Dimethylbenzimidazole;521
42.3.3;Many References to Previous Work Will be Found in the Last Two Papers;522
43;Chapter 39: Interactions Between Proteins and DNA;523
43.1;DNA-Binding Proteins;523
43.2;Study of the Protein-DNA Complexes;525
43.3;Some Other Types of DNA-Binding Proteins;531
43.4;Selected References;534
43.4.1;Trp Repressor. Structural Aspects;534
43.4.2;Met Repressor;534
44;Chapter 40: Evolution of Biosynthetic Pathways;535
44.1;Principles of Protein Evolution;535
44.2;Two Theories for the Evolution of Biosynthetic Pathways;535
44.3;The Methionine and Cysteine Biosynthetic Pathways;536
44.4;The Threonine, Isoleucine, Cysteine and Tryptophan Biosynthetic Pathways;539
44.5;The Evolutionary Pathway Leading to the Three Isofunctional Aspartokinases in Escherichia coli;545
44.6;Transmembrane Facilitators;552
44.7;DNA-Binding Regulator Proteins;553
44.8;Selected References;553
44.8.1;Two Books;553
44.8.2;Two Different Theories on the Evolution of Biosynthetic Pathways;553
44.8.3;Common Origin of Cystathionine-gamma-Synthase and Cystathionase;553
44.8.4;Common Origin of Threonine Synthase, Threonine Dehydratase, D-Serine Dehydratase, and the B Chain of Tryptophan Synthase;554
44.8.5;Comparison of arg Genes with Homologous and Analogous Enzymes;554
44.8.6;Evolution of the E. coli Aspartokinases and Homoserine Dehydrogenases;554
44.8.7;Structural and Evolutionary Relationships Between E. coli Aspartokinase-Homoserine Dehydrogenases and Monofunctional Homoserine;554
44.8.8;Superfamily of Transmembrane Facilitators;554
44.8.9;DNA-Binding Regulator Proteins;554
45;Index;555