A Genetic Switch, Phage Lambda Revisited

by Ptashne, Mark

• ISBN13: 9780879697167
• ISBN10: 0879697164
• Edition: 3rd
• Format: Paperback
• Copyright: 2004-04-08
• Publisher: Cold Spring Harbor Laboratory Press

Summary

The first edition of Mark Ptashne's 1986 book describing the principles of gene regulation in phage lambda became a classic in both content and form, setting a standard of clarity and precise prose that has rarely been bettered. This edition is a reprint of the original text, together with a new chapter updating the story to 2004. Among the striking new developments are recent findings on long#x13;range interactions between proteins bound to widely separated sites on the phage genome, and a detailed description of how gene activation works.

Table of Contents

Preface to the Third Edition,	xi
Preface to the First Edition,	xiii
INTRODUCTION	1	(10)
CHAPTER ONE THE MASTER ELEMENTS OF CONTROL	11	(20)
Components of the Switch	14	(4)
DNA	14	(1)
RNA Polymerase	15	(1)
The Repressor	16	(1)
Cro	17	(1)
The Action of Repressor and Cro	18	(4)
Negative Control	18	(1)
Positive Control	18	(2)
Cooperativity of Repressor Binding	20	(2)
Induction-Flipping the Switch	22	(4)
Cooperativity-Switch Stability and Sensitivity	26	(2)
The Effect of Autoregulation	28	(1)
Other Cases	28	(3)
CHAPTER TWO PROTEIN-DNA INTERACTIONS AND GENE CONTROL	31	(16)
The Operator	31	(3)
Repressor	34	(3)
Cro	37	(2)
Amino Acid-Base Pair Interactions	39	(4)
The Promoter	43	(1)
Gene Control	44	(3)
CHAPTER THREE CONTROL CIRCUITS-SETTING THE SWITCH	47	(20)
A Brief Overview of λ Growth	48	(4)
The Genetic Map	48	(1)
Circularization	49	(1)
Gene Expression	50	(1)
Integration	51	(1)
Control of Transcription	52	(4)
Very Early	52	(1)
Early	52	(1)
Late Lytic	53	(2)
Late Lysogenic	55	(1)
The Decision	56	(1)
Control of Integration and Excision	57	(3)
Case 1-Establishing Lysogeny	58	(1)
Case 2-Lytic Growth	58	(1)
Case 3-Induction	58	(2)
Other Phages	60	(1)
The SOS Response	60	(2)
λ Pathways and Cell Development	62	(5)
Regulatory Genes	62	(1)
Switches	63	(1)
Patterns of Gene Expression	64	(3)
CHAPTER FOUR HOW DO WE KNOW-THE KEY EXPERIMENTS	67	(42)
The Repressor Idea	67	(4)
Clear and Virulent Mutants	67	(2)
Observations	67	(1)
Explanation	68	(1)
Immunity and Heteroimmunity	69	(1)
Observations	69	(1)
Explanation	70	(1)
Asymmetry in Bacterial Mating	70	(6)
Observations	70	(1)
Explanation	71	(1)
The Repressor Problem in the Early 1960's	71	(1)
Repressor Isolation and DNA Binding	72	(2)
Making More Repressor	74	(2)
The Claims of Chapters One and Two	76	(27)
The repressor is composed of two globular domains held together by a linker of some 40 amino acids	76	(1)
The repressor dimerizes, largely through interaction between Its carboxyl domains	76	(2)
A repressor dimer binds, through Its amino domains, to a 17 base pair operator site	78	(6)
A single operator site binds one dimer of repressor	78	(2)
Dimers form before DNA binding	80	(2)
The amino domains contact DNA	82	(2)
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	84	(2)
Chemical probes	84	(1)
Operator mutations	85	(1)
Binding to supercoiled and linear DNA	85	(1)
Repressor binds to three sites in OR with alternate pairwise cooperativity. The cooperativity is mediated by interactions between carboxyl domains of adjacent dimers	86	(1)
In a lysogen repressor is typically bound to OR1 and OR2. The bound repressors turn off rightward transcription of cro and stimulate leftward transcription of cl. At higher concentrations, repressor binds to OR3 to turn off transcription of cl	87	(5)
Cro binds first to OR3, then to OR1 and OR2, thereby first turning off PRS, then PR	92	(2)
Some background about Cro	92	(1)
Cro in vivo	93	(1)
Cro in vitro	94	(1)
RecA cleaves repressor to trigger induction	94	(1)
When Cro is bound at 0R3 the switch is thrown	95	(1)
Repressor and Cro bind to the operator as shown in Figures 2.6, 2.8, 2.10, and 2.11	95	(4)
Crystallography	95	(1)
The "helix swap" experiment	96	(2)
Specific amino acid-base pair contacts	98	(1)
The role of the arm of λ repressor	99	(1)
Repressor activates transcription of cl by binding to OR2 and contacting polymerase with its amino domain	99	(10)
Positive control mutants	99	(3)
Positive control in vitro	102	(1)
Conclusion	103	(6)
CHAPTER FIVE 2004: NEW DEVELOPMENTS	109	(42)
1. Long-range Cooperativity and Repression of PRM	109	(13)
An Octamer of Repressor Binds OR and O,	110	(2)
Autonegative Regulation of Repressor Synthesis	112	(1)
How Do We Know	113	(9)
Long-range Interactions and Repression of PR	113	(1)
Long-range Interactions and Repression of PRM	114	(1)
Activation and Repression of PRM	114	(1)
Repressor Structure	115	(7)
2. Positive Control (Activation of Transcription)	122	(9)
Polymerase and Promoter	122	(1)
The Mechanism of Activation	123	(1)
How Do We Know	123	(8)
Activating Region Variants	123	(2)
A Suppressor of a pc Mutant	125	(1)
Crystallography	125	(1)
Activator Bypass	125	(2)
Changing Activating Regions and Target Context	127	(4)
3. The Structure of the Repressor Monomer and the Mechanism of Repressor Cleavage	131	(2)
How Do We Know	132	(1)
4. Evolving the Switch	133	(3)
Changing the Affinities of Sites in OR for Repressor	133	(1)
Eliminating Positive Control	134	(1)
Eliminating Cooperativity between DNA-binding Dimers	134	(2)
5. CII and the Decision	136	(15)
Index	151