Galactose Regulon of Yeast: From Genetics to Systems Biology / Edition 1

Galactose Regulon of Yeast: From Genetics to Systems Biology / Edition 1

by Paike Jayadeva Bhat

The galactose regulon of yeast is one of the best studied regulons. It is an ideal paradigm for demonstrating fundamental and evolving concepts in biology and is used in this book as a model system to explain various facets of conventional and modern biology.

The book starts with a brief historical overview on yeast research, i.e. early observations in enzyme

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The galactose regulon of yeast is one of the best studied regulons. It is an ideal paradigm for demonstrating fundamental and evolving concepts in biology and is used in this book as a model system to explain various facets of conventional and modern biology.

The book starts with a brief historical overview on yeast research, i.e. early observations in enzyme adaptation, classical genetics, formulating hypotheses based on genetic inference. This is followed by molecular genetics of the galactose regulon, isolation of genes and testing of the hypotheses. The power of mutational analysis in deciphering molecular mechanisms is conveyed. Further, contemporary topics such as genomics, evolution, single cell analysis of transcriptional switching, binary and graded responses, biological consequences of feed back regulation in genetic circuits, and stochasticity are addressed.

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Springer Berlin Heidelberg
Publication date:
Edition description:
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6.10(w) x 9.30(h) x 0.50(d)

Table of Contents

Introduction     1
An Overview     1
A General Perspective     1
An Aside on Analogy     2
References     3
Yeast is a Eukaryotic Model Organism     4
Introduction     4
Model Organisms     4
Yeast     5
Life Cycle of Haploid Yeast     7
Life Cycle of Diploid Yeast     9
Information Transfer from Parents to Descendents     9
Human Life Cycle     13
References     14
A Cell as a Biochemical Entity     15
Introduction     15
Chemical Constituents     15
Macroscopic and Microscopic Aspects of Metabolism     16
Biochemical Transactions     17
Energy Transactions     19
References     23
Adaptation to Environment     25
Growth and Multiplication     25
Introduction     25
Growth Kinetics     25
Effect of Nutrients on Growth     28
Metabolic Strategy     29
References     33
Enzyme Adaptation     33
Introduction     33
Adaptation to Nutrients     33
Long-Term Adaptation     35
Single-Cell Analysis of Long-Term Adaptation     36
Galactose Metabolism     38
References     41
Induction of Leloir Enzymes     42
Introduction     42
Galactose Induces the Synthesis of Leloir Enzymes     43
Galactose Activates the Transcription of GAL Genes     43
Galactose Activates a Genetic Program     46
References     47
Genetic Dissection of Galactose Metabolism     49
Genetic Analysis of GAL Regulon     49
Introduction     49
Mutant Hunt     49
Segregation Analysis     50
Complementation Analysis     50
Concept of an Allele     54
Special Cases of Complementation     56
Aberrant Segregation and Recombination Model     58
References     61
Genetic Mapping of GAL Genes     62
Introduction     62
Tetrad Analysis     62
Mapping of GAL Genes by Tetrad Analysis     64
Map Distance and Recombination Frequency     67
An Aside on Mapping of Human Genes by Linkage Analysis     69
References     76
Genetic Analysis GAL Genetic Switch     79
Negative Control by the Repressor     79
Introduction     79
Discovery of a Repressor of GAL Regulon     80
Reference     82
Operator Repressor Model of GAL Regulon     82
Introduction     82
Testing the Predictions of the Model     82
References     84
Genetic Interactions     85
Introduction     85
Recessivity and Dominance     85
Negative Dominance     87
Epistasis     87
Allele-Specific Interactions     89
References     90
Conditional Lethal Mutations     90
Introduction     90
Temperature-Sensitive Allele of GAL3     91
Temperature-Sensitive Allele of GAL4     92
References     93
Revised Model of GAL Genetic Switch     94
Introduction     94
Protein-Protein Interaction Model     94
Interaction Between GAL4 and GAL80 Proteins     95
References     97
Signal Transduction in GAL Regulon     97
Introduction     97
Catalytic Model     98
References      99
Molecular Genetics of GAL Regulon     101
Cloning: A Perspective     101
Introduction     101
Vectors, Genetic Transformation, and Recombinant DNA Technology     102
DNA Cloning     104
Genomic DNA Library     105
cDNA Library     105
Isolation of Recombinant Clones     106
Development of Yeast Shuttle Vectors     107
References     110
Genomic Organization of GAL Cluster     110
Introduction     110
Cloning of the GAL Cluster     111
Analysis of GALI-10 Intergenic Region     113
References     118
Isolation of GAL4: The Transcriptional Activator     118
Introduction     118
Cloning of GAL4 by Functional Complementation     120
GAL4 Protein Binds Upstream Activating Sequences     120
GAL4 Protein Binds GAL80 Protein     123
GAL4 Protein is Modular     124
References     129
Isolation of GAL80: The Repressor     131
Introduction     131
Cloning of GAL80 by Genetic Suppression     131
Autogenous Regulation of GAL80 Expression     132
Mutational Analysis of GAL80      133
References     134
Isolation of GAL3: The Signal Transducer     135
Introduction     135
Cloning of GAL3     135
GAL1 and GAL3 are Paralogues     137
GAL1 is a Degenerate Signal Transducer     137
Autogenous Regulation of GAL3 Expression     138
An aside on Positional Cloning     138
Restriction Fragment Length Polymorphism     141
References     141
Signal Transduction Revisited     143
Revised Model of Signal Transduction     143
Introduction     143
Protein-Protein Interaction Model     143
Testing the Predictions of the Protein-Protein Interaction Model     144
Recent Analysis of Signal Transduction     145
References     150
Genetic Dissection of Signal Transduction     150
Introduction     150
Mutational Analysis of GAL3     151
Mutational Analysis of GAL80     154
References     155
Versatile Galactose Genetic Switch     157
Transcription Activation     157
Introduction     157
RNA Polymerase II     158
Transcriptional Activation by Recruitment      159
References     164
Glucose Repression     164
Introduction     164
MIG1 Protein is a DNA-Binding Transcriptional Repressor     165
Combined Role of GAL80 and MIG1 Proteins in Glucose Repression     165
Binary and Graded Response     166
GAL4 Expression is Repressed by Glucose     169
References     170
Fine Regulation of GAL Genetic Switch     170
Introduction     170
Basal and Induced Expression     171
Post-Translational Modification of GAL4 Protein     173
References     174
Paradigmatic Role of Galactose Switch     175
GAL Regulon and Genomics     175
Introduction     175
Functional Profiling of Fitness     177
Analysis Genome-Wide DNA Binding     179
Genomic Approach for Network Analysis     180
References     183
GAL Regulon and Systems Biology     183
Introduction     183
Quantitative Basis of GAL Genetic Switch     184
Long-Term Adaptation Revisited     188
Feedback Loops of GAL Regulon     190
References     193
Galactose Metabolism and Evolution      193
Introduction     193
Evolution of Galactose Metabolism     194
Evolution of Genomic Organization of Galactose Metabolic Enzymes     196
Adaptive Evolution of Galactose Metabolism     197
Evolution of Regulatory Network of Galactose Metabolism     199
Genome Duplication in Saccharomyces     200
References     201
GAL Switch as a Tool     202
Introduction     202
High-level Protein Expression     202
Dihybrid Analysis     203
Dihybrid Approach for Genetic Analysis     204
Genome-Wide Protein-Protein Interaction     206
GAL Switch as a Tool in Higher Organisms     207
References     208
Lessons Learned     208
Introduction     208
Robustness and Fragility     210
Stochasticity and Phenotypic Variation     211
References     214
Index     215

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