Preface to the Third Edition | p. xi |
Preface to the First Edition | p. xiii |
Introduction | p. 1 |
The Master Elements of Control | p. 11 |
Components of the Switch | p. 14 |
DNA | p. 14 |
RNA Polymerase | p. 15 |
The Repressor | p. 16 |
Cro | p. 17 |
The Action of Repressor and Cro | p. 18 |
Negative Control | p. 18 |
Positive Control | p. 18 |
Cooperativity of Repressor Binding | p. 20 |
Induction--Flipping the Switch | p. 22 |
Cooperativity--Switch Stability and Sensitivity | p. 26 |
The Effect of Autoregulation | p. 28 |
Other Cases | p. 28 |
Protein-DNA Interactions and Gene Control | p. 31 |
The Operator | p. 31 |
Repressor | p. 34 |
Cro | p. 37 |
Amino Acid-Base Pair Interactions | p. 39 |
The Promoter | p. 43 |
Gene Control | p. 44 |
Control Circuits--Setting the Switch | p. 47 |
A Brief Overview of [lambda] Growth | p. 48 |
The Genetic Map | p. 48 |
Circularization | p. 49 |
Gene Expression | p. 50 |
Integration | p. 51 |
Control of Transcription | p. 52 |
Very Early | p. 52 |
Early | p. 52 |
Late Lytic | p. 53 |
Late Lysogenic | p. 55 |
The Decision | p. 56 |
Control of Integration and Excision | p. 57 |
Establishing Lysogeny | p. 58 |
Lytic Growth | p. 58 |
Induction | p. 58 |
Other Phages | p. 60 |
The SOS Response | p. 60 |
[lambda] Pathways and Cell Development | p. 62 |
Regulatory Genes | p. 62 |
Switches | p. 63 |
Patterns of Gene Expression | p. 64 |
How Do We Know--the Key Experiments | p. 67 |
The Repressor Idea | p. 67 |
Clear and Virulent Mutants | p. 67 |
Observations | p. 67 |
Explanation | p. 68 |
Immunity and Heteroimmunity | p. 69 |
Observations | p. 69 |
Explanation | p. 70 |
Asymmetry in Bacterial Mating | p. 70 |
Observations | p. 70 |
Explanation | p. 71 |
The Repressor Problem in the Early 1960s | p. 71 |
Repressor Isolation and DNA Binding | p. 72 |
Making More Repressor | p. 74 |
The Claims of Chapters One and Two | p. 76 |
The repressor is composed of two globular domains held together by a linker of some 40 amino acids | p. 76 |
The repressor dimerizes, largely through interaction between its carboxyl domains | p. 76 |
A repressor dimer binds, through its amino domains, to a 17 base pair operator site | p. 78 |
A single operator site binds one dimer of repressor | p. 78 |
Dimers form before DNA binding | p. 80 |
The amino domains contact DNA | p. 82 |
There are three 17 base pair repressor binding sites in the right operator. At each site repressor and Cro bind along the same face of the helix | p. 84 |
Chemical probes | p. 84 |
Operator mutations | p. 85 |
Binding to supercoiled and linear DNA | p. 85 |
Repressor binds to three sites in O[subscript R] with alternate pairwise cooperativity. The cooperativity is mediated by interactions between carboxyl domains of adjacent dimers | p. 86 |
In a lysogen repressor is typically bound to O[subscript R]1 and O[subscript R]2. The bound repressors turn off rightward transcription of cro and stimulate leftward transcription of cl. At higher concentrations, repressor binds to O[subscript R]3 to turn off transcription of cl | p. 87 |
Cro binds first to O[subscript R]3, then to O[subscript R]1 and O[subscript R]2, thereby first turning off P[subscript RM], then P[subscript R] | p. 92 |
Some background about Cro | p. 92 |
Cro in vivo | p. 93 |
Cro in vitro | p. 94 |
RecA cleaves repressor to trigger induction | p. 94 |
When Cro is bound at O[subscript R]3 the switch is thrown | p. 95 |
Repressor and Cro bind to the operator as shown in Figures 2.6, 2.8, 2.10, and 2.11 | p. 95 |
Crystallography | p. 95 |
The "helix swap" experiment | p. 96 |
Specific amino acid-base pair contacts | p. 98 |
The role of the arm of [lambda] repressor | p. 99 |
Repressor activates transcription of cl by binding to O[subscript R]2 and contacting polymerase with its amino domain | p. 99 |
Positive control mutants | p. 99 |
Positive control in vitro | p. 102 |
Conclusion | p. 103 |
2004: New Developments | p. 109 |
Long-range Cooperativity and Repression of P[subscript RM] | p. 109 |
An Octamer of Repressor Binds O[subscript R] and O[subscript L] | p. 110 |
Autonegative Regulation of Repressor Synthesis | p. 112 |
How Do We Know | p. 113 |
Long-range Interactions and Repression of P[subscript R] | p. 113 |
Long-range Interactions and Repression of P[subscript RM] | p. 114 |
Activation and Repression of P[subscript RM] | p. 114 |
Repressor Structure | p. 115 |
Positive Control (Activation of Transcription) | p. 122 |
Polymerase and Promoter | p. 122 |
The Mechanism of Activation | p. 123 |
How Do We Know | p. 123 |
Activating Region Variants | p. 123 |
A Suppressor of a pc Mutant | p. 125 |
Crystallography | p. 125 |
Activator Bypass | p. 125 |
Changing Activating Regions and Target Context | p. 127 |
The Structure of the Repressor Monomer and the Mechanism of Repressor Cleavage | p. 131 |
How Do We Know | p. 132 |
Evolving the Switch | p. 133 |
Changing the Affinities of Sites in O[subscript R] for Repressor | p. 133 |
Eliminating Positive Control | p. 134 |
Eliminating Cooperativity between DNA-binding Dimers | p. 134 |
CII and the Decision | p. 136 |
Index | p. 151 |
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