A Genetic Switch, Third Edition: Phage Lambda Revisited

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-range interactions between proteins bound to widely separated sites on the phage genome, and a detailed description of how gene activation works. INTRODUCTION CHAPTER ONE THE MASTER ELEMENTS OF CONTROL Components of the Switch DNA RNA Polymerase The Repressor Cro The Action of Repressor and Cro Negative Control Positive Control Cooperativity of Repressor Binding Induction—Flipping the Switch Cooperativity—Switch Stability and Sensitivity The Effect of Autoregulation Other Cases CHAPTER TWO PROTEIN-DNA INTERACTIONS AND GENE CONTROL The Operator Repressor Cro Amino Acid-Base Pair Interactions The Promoter Gene Control CHAPTER THREE CONTROL CIRCUITS—SETTING THE SWITCH A Brief Overview of λ Growth The Genetic Map Circularization Gene Expression Integration Control of Transcription Very Early Early Late Lytic Late Lysogenic The Decision Control of Integration and Excision Case 1—Establishing Lysogeny Case 2—Lytic Growth Case 3—Induction Other Phages The SOS Response λ Pathways and Cell Development Regulatory Genes Switches Patterns of Gene Expression CHAPTER FOUR HOW DO WE KNOW—THE KEY EXPERIMENTS The Repressor Idea Clear and Virulent Mutants Observations Explanation Immunity and Heteroimmunity Observations Explanation Asymmetry in Bacterial Mating Observations Explanation The Repressor Problem in the Early 1960s Repressor Isolation and DNA Binding Making More Repressor The Claims of Chapters One and Two The repressor is composed of two globular domains held together by a linker of some 40 amino acids The repressor dimerizes, largely through interaction between its carboxyl domains A repressor dimer binds, through its amino domains, to a 17 base pair operator site A single operator site binds one dimer of repressor Dimers form before DNA binding The amino domains contact DNA 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 Chemical probes Operator mutations Binding to supercoiled and linear DNA Repressor binds to three sites in OR with alternate pairwise cooperativity. The cooperativity is mediated by interactions between carboxyl domains of adjacent dimers 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 cI. At higher concentrations, repressor binds to OR3 to turn off transcription of cI Cro binds first to OR3, then to OR1 and OR2, thereby first turning off PRM, then PR Some background about Cro Cro in vivo Cro in vitro RecA cleaves repressor to trigger induction When Cro is bound at OR3 the switch is thrown Repressor and Cro bind to the operator as shown in Figures 2.6, 2.8, 2.10, and 2.11 Crystallography The “helix swap” experiment Specific amino acid-base pair contacts The role of the arm of λ repressor Repressor activates transcription of cI by binding to OR2 and contacting polymerase with its amino domain Positive control mutants Positive control in vitro Conclusion CHAPTER FIVE 2004: NEW DEVELOPMENTS 1. Long-range Cooperativity and Repression of PRM An Octamer of Repressor Binds OR and OL Autonegative Regulation of Repressor Synthesis How Do We Know Long-range Interactions and Repression of PR Long-range Interactions and Repression of PRM Activation and Repression of PRM Repressor Structure 2. Positive Control (Activation of Transcription) Polymerase and Promoter The Mechanism of Activation How Do We Know Activating Region Variants A Suppressor of a pc Mutant Crystallography Activator Bypass Changing Activating Regions and Target Context 3. The Structure of the Repressor Monomer and the Mechanism of Repressor Cleavage How Do We Know 4. Evolving the Switch Changing the Affinities of Sites in OR for Repressor Eliminating Positive Control Eliminating Cooperativity between DNA-binding Dimers 5. CII and the Decision "The first edition of A Genetic Switch has become a classic exposition of gene regulation, explaining in simple molecular terms how proteins bind DNA and turn genes on and off as the virus lambda grows in bacteria. To that original text, reprinted here with small modifications, the author has added a chapter describing recent advances that extend and deepen our understanding of lambda's "genetic switch." The study of lambda reveals the basic reactions that underlie transcriptional regulation in all organisms and shows how those reactions can be combined to produce a complex regulatory circuit."--BOOK JACKET. This updated third edition focuses once again solely on phage, incorporating the most recent insights into gene expression in prokaryotes while retaining all the qualities of the original edition