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