Galactose Regulon of Yeast: From Genetics to Systems Biology

Contents......Page 8
1.1.1 A General Perspective......Page 14
1.1.2 An Aside on Analogy......Page 15
References......Page 16
1.2.2 Model Organisms......Page 17
1.2.3 Yeast......Page 18
1.2.4 Life Cycle of Haploid Yeast......Page 20
1.2.6 Information Transfer from Parents to Descendents......Page 22
1.2.7 Human Life Cycle......Page 26
References......Page 27
1.3.2 Chemical Constituents......Page 28
1.3.3 Macroscopic and Microscopic Aspects of Metabolism......Page 29
1.3.4 Biochemical Transactions......Page 30
1.3.5 Energy Transactions......Page 32
References......Page 36
2.1.2 Growth Kinetics......Page 37
2.1.3 Effect of Nutrients on Growth......Page 40
2.1.4 Metabolic Strategy......Page 41
2.2.2 Adaptation to Nutrients......Page 45
2.2.3 Long-Term Adaptation......Page 47
2.2.4 Single-Cell Analysis of Long-Term Adaptation......Page 48
2.2.5 Galactose Metabolism......Page 50
References......Page 53
2.3.1 Introduction......Page 54
2.3.3 Galactose Activates the Transcription of GAL Genes......Page 55
2.3.4 Galactose Activates a Genetic Program......Page 58
References......Page 59
3.1.2 Mutant Hunt......Page 60
3.1.4 Complementation Analysis......Page 61
3.1.5 Concept of an Allele......Page 65
3.1.6 Special Cases of Complementation......Page 67
3.1.7 Aberrant Segregation and Recombination Model......Page 69
References......Page 72
3.2.2 Tetrad Analysis......Page 73
3.2.3 Mapping of GAL Genes by Tetrad Analysis......Page 75
3.2.4 Map Distance and Recombination Frequency......Page 78
3.2.5 An Aside on Mapping of Human Genes by Linkage Analysis......Page 80
References......Page 87
4.1.1 Introduction......Page 89
4.1.2 Discovery of a Repressor of GAL Regulon......Page 90
4.2.2 Testing the Predictions of the Model......Page 92
References......Page 94
4.3.2 Recessivity and Dominance......Page 95
4.3.4 Epistasis......Page 97
4.3.5 Allele-Specifi c Interactions......Page 99
4.4.1 Introduction......Page 100
4.4.2 Temperature-Sensitive Allele of GAL3......Page 101
4.4.3 Temperature-Sensitive Allele of GAL4......Page 102
References......Page 103
4.5.2 Protein–Protein Interaction Model......Page 104
4.5.3 Interaction Between GAL4 and GAL80 Proteins......Page 105
4.6.1 Introduction......Page 107
4.6.2 Catalytic Model......Page 108
References......Page 109
5.1.1 Introduction......Page 111
5.1.2 Vectors, Genetic Transformation, and Recombinant DNA Technology......Page 112
5.1.3 DNA Cloning......Page 114
5.1.5 cDNA Library......Page 115
5.1.6 Isolation of Recombinant Clones......Page 116
5.1.7 Development of Yeast Shuttle Vectors......Page 117
5.2.1 Introduction......Page 120
5.2.2 Cloning of the GAL Cluster......Page 121
5.2.3 Analysis of GAL1-10 Intergenic Region......Page 123
5.3.1 Introduction......Page 128
5.3.3 GAL4 Protein Binds Upstream Activating Sequences......Page 130
5.3.4 GAL4 Protein Binds GAL80 Protein......Page 133
5.3.5 GAL4 Protein is Modular......Page 134
References......Page 139
5.4.2 Cloning of GAL80 by Genetic Suppression......Page 141
5.4.3 Autogenous Regulation of GAL80 Expression......Page 142
5.4.4 Mutational Analysis of GAL80......Page 143
References......Page 144
5.5.2 Cloning of GAL3......Page 145
5.5.4 GAL1 is a Degenerate Signal Transducer......Page 147
5.5.6 An aside on Positional Cloning......Page 148
References......Page 151
6.1.2 Protein–Protein Interaction Model......Page 153
6.1.3 Testing the Predictions of the Protein–Protein Interaction Model......Page 154
6.1.4 Recent Analysis of Signal Transduction......Page 155
6.2.1 Introduction......Page 160
6.2.2 Mutational Analysis of GAL3......Page 161
6.2.3 Mutational Analysis of GAL80......Page 164
References......Page 165
7.1.1 Introduction......Page 167
7.1.2 RNA Polymerase II......Page 168
7.1.3 Transcriptional Activation by Recruitment......Page 169
7.2.1 Introduction......Page 174
7.2.3 Combined Role of GAL80 and MIG1 Proteins in Glucose Repression......Page 175
7.2.4 Binary and Graded Response......Page 176
7.2.5 GAL4 Expression is Repressed by Glucose......Page 179
7.3.1 Introduction......Page 180
7.3.2 Basal and Induced Expression......Page 181
7.3.3 Post-Translational Modifi cation of GAL4 Protein......Page 183
References......Page 184
8.1.1 Introduction......Page 185
8.1.2 Functional Profi ling of Fitness......Page 187
8.1.3 Analysis Genome-Wide DNA Binding......Page 189
8.1.4 Genomic Approach for Network Analysis......Page 190
8.2.1 Introduction......Page 193
8.2.2 Quantitative Basis of GAL Genetic Switch......Page 194
8.2.3 Long-Term Adaptation Revisited......Page 198
8.2.4 Feedback Loops of GAL Regulon......Page 200
8.3.1 Introduction......Page 203
8.3.2 Evolution of Galactose Metabolism......Page 204
8.3.3 Evolution of Genomic Organization of Galactose Metabolic Enzymes......Page 206
8.3.4 Adaptive Evolution of Galactose Metabolism......Page 207
8.3.5 Evolution of Regulatory Network of Galactose Metabolism......Page 209
8.3.6 Genome Duplication in Saccharomyces......Page 210
References......Page 211
8.4.2 High-level Protein Expression......Page 212
8.4.3 Dihybrid Analysis......Page 213
8.4.4 Dihybrid Approach for Genetic Analysis......Page 214
8.4.5 Genome-Wide Protein–Protein Interaction......Page 216
8.4.6 GAL Switch as a Tool in Higher Organisms......Page 217
8.5.1 Introduction......Page 218
8.5.2 Robustness and Fragility......Page 220
8.5.3 Stochasticity and Phenotypic Variation......Page 221
References......Page 224
C......Page 225
G......Page 226
O......Page 227
S......Page 228
Z......Page 229