Regulation of Gene Expression in Escherichia coli

Book by None

1. Introduction: From Physiology to DNA and Back.- 2. RNA Chain Initiation and Promoter Escape by RNA Polymerase.- Promoter Function is Regulated at Two Distinct Phases of Transcription: Promoter Binding and RNA Chain Initiation.- The Biochemistry of the RNA Chain Initiation Phase of Transcription.- Parameters That Describe the RNA Chain Initiation Reaction at Different Promoters.- Factors That Affect the Initiation Reaction: Intrinsic Factors.- Factors That Affect the Initiation Reaction: Extrinsic Factors.- Models for the Mechanism of RNA Chain Initiation: Some Simple Models Do Not Account for What Is Known.- Models for the Mechanism of RNA Chain Initiation-Models Based on Recent Models for RNA Chain Elongation.- 3. Transcription Termination and Its Control.- Termination.- Antitermination.- 4. Codon Context, Translational Step-Times and Attenuation.- Overview.- Attenuation.- Codon Context and Translational Efficiency.- Effects of Codon Pair Bias on Translational Step-Times.- Discussion.- 5. Control by Antisense RNA.- Antisense RNAs Control Diverse Biological Functions.- Antisense RNAs Control Gene Expression at Many Different Post-Transcriptional Levels.- Antisense RNAs Pair to Their Target RNAs by Defined Mechanisms.- Overview.- 6. Translational Control of Gene Expression in E. Coli and Bacteriophage.- Translation Initiation.- Translational Operators.- Translational Repressors.- Mechanisms of Control.- Translational Control and mRNA Processing and/or Degradation.- The Role of Translational Control in Growth Rate Regulation.- Conclusions and Perspectives.- 7. Effects of DNA Supercoiling on Gene Expression.- Synopsis.- The Dependence of Transcription on the Cellular Level of DNA Gyrase and DNA Topoisomerase I.- Mechanistic Considerations.- Supercoiling of the DNA Template by Transcription.- Concluding Remarks.- 8. The HU and IHF Proteins: Accessory Factors for Complex Protein-DNA Assemblies.- Perspective.- Structure.- Interaction with Nucleic Acids.- Control of Intracellular Concentration and Activity.- Participation of IHF and HU in Well-Characterized Biochemical Processes.- Unfinished Business.- 9. The lac and gal Operons Today.- The lac and gal Operons Encode Enzymes of a Continuous Biochemical Pathway.- The Regulatory Circuits and Their Components.- Modulation of Promoters by cAMP•CRP.- Control of P2 by UTP in gal.- Natural Polarity.- Negative Control by Repressor-Operator Interactions.- Epilogue.- 10. The Maltose System.- and Scope.- The Positive Transcriptional Activator MalT.- The Maltose/Maltodextrin Transport System.- The Enzymes of the Maltose System.- Nonclassical Regulatory Phenomena.- Perspectives.- 11. The Phosphoenolpyruvate-Dependent Carbohydrate: Phosphotransferase System (PTS) and Control of Carbon Source Utilization.- Regulatory Phenomena Related to Carbon Source Utilization.- Bacterial Transport Systems and Global Regulatory Networks Form a Unit.- The Bacterial PTS Is a Transport and Signal Transduction System.- IIAGlc of the PTS Is Central to Carbon Catabolite Repression.- IIAGlc, the Regulation of Adenylate Cyclase Activity and of Intracellular cAMP Levels.- Not Only cAMP Levels, but Also CRP Levels Are Essential in Catabolite Repression.- IIAGlc and Inducer Exclusion.- Catabolite Repression and Inducer Exclusion Act in Concert.- Carbon Catabolite Repression through PTS-Control Is Part of a Stimulon.- Concluding Remarks.- 12. The Cap Modulon.- The Long History of CAP.- Cyclic AMP and Gene Expression.- CAP as a Global Regulator: The CAP Modulon.- CAP Binding at Target Promoters and Structural Studies.- Activation by CAP at “Simple” Promoters.- Activation by CAP at Complex Promoters.- CAP as a Repressor and a Co-Repressor.- CAP: Paradigm or Artifact?.- 13. Regulation of Nitrogen Assimilation.- The glnALG(glnA ntrBC) Operon.- The ?54-Dependent Promoter.- Transcriptional Enhancers.- Phosphorylation of NRI.- NRI/NRII as Two-Component Paradigm.- Activation of Transcription.- Response to Nitrogen Availability.- 14. History of the Pho System.- 15. Are the Multiple Signal Transduction Pathways of the Pho Regulon Due to Cross Talk or Cross Regulation?.- Genes for Pi Control of the Pho Regulon.- Transmembrane Signaling by Environmental Pi.- Genes for Pi Independent Controls of the Pho Regulon.- Activation by CreC and Acetyl Phosphate.- Cross Talk, Cross Regulation and a Hypothesis.- Is There Evidence for Cross Regulation?.- Overview and Prospects for Future Studies.- 16. The FNR Modulon and FNR-Regulated Gene Expression.- The Metabolic Arena.- The FNR Modulon.- The FNR Protein and Relationships with CAP.- The DNA-Binding Specificity of FNR.- In Vitro Transcription Activation and Repression.- Transcriptional Organization of Representative Promoters.- Potential FNR Contacts with RNA Polymerase and DNA-Bending.- The Mystery of Redox-Sensing.- Structural and Functional Homologs of FNR.- Concluding Remarks.- 17. The NAR Modulon Systems: Nitrate and Nitrite Regulation of Anaerobic Gene Expression.- Anaerobic Respiration.- The Characterization of the Nar Regulatory System.- Dual Two-Component Regulatory Systems.- The Role of Nitrite in the Nar Regulatory System.- The Sensor Proteins.- The Response Regulators.- Indirect Nitrate Regulation of Gene Expression.- Concluding Remarks.- 18. Regulation of Aerobic and Anaerobic Metabolism by the Arc System.- Identification of the arc Genes.- In Vivo Studies of arc Mutants.- In Vitro Phosphorylation Studies.- The Arc Modulon.- ArcA DNA Binding.- The Arc Stimulus.- Future Studies.- 19. The Porin Regulon: A Paradigm for the Two-Component Regulatory Systems.- Background.- The History of Porin Regulation.- The Structure of the ompB Locus.- The Structure of the ompF and ompC Genes.- The Roles of OmpR and EnvZ.- Phosphorylation and Signal Transduction.- Summary and Conclusions.- 20. The Leucine\Lrp Regulon.- The Leucine-Responsive Regulatory Protein.- Regulation of Lrp Synthesis.- Target Operons of Lrp and Mutant Phenotypes.- Lrp as a Chromosome Organizer.- Molecular Aspects of Lrp Interactions at Individual Promoters.- 21. Adaptive responses to Oxidative Stress: The soxRS and oxyR Regulons.- Reactive Oxygen Species.- Antioxidant Defenses.- Oxidative Stress.- Global Responses to Oxidative Stress.- The soxRS Regulon.- The oxyR Regulon.- Control of Antibiotic Resistance Genes.- 22. The SOS Regulatory System.- and Current Regulatory Model.- Development of the SOS Model.- Recent Developments.- Behavior of the SOS Gene Regulatory Circuitry.- Future Prospects.- 23. Heat Shock Regulation.- Properties of Important Heat Shock Proteins.- Regulation of the ?32-Promoted Heat Shock Response.- A Second Heat Shock Regulon.- The ?54-Promoted Stress Response.- Heat Shock or Stress Responses in Other Eubacteria.- 24. Roles for Energy-Dependent Proteases in Regulatory Cascades.- The Proteases and Their Targets.- Summary and General Conclusions.- 25. Control of rRNA and Ribosome Synthesis.- rRNA Gene Organization.- High Activity of rRNA Synthesis Rates.- Stringent Control.- Growth Rate Dependent Control.- Additional Considerations.- Conclusion and Future Prospects.- 26. Cell Division.- The Cell Division Process.- Essential Cell Division Genes.- Transcriptional Regulation of Cell Division Genes.- Translational Control.- Division Inhibitors.- Cell Division Inhibition by Mutations in Genes That Do Not Code for Cell Division Proteins.- Past, Present and Future.- 27. Regulation of Gene Expression in Stationary Phase.- The ?s Regulon.- RpoS Regulation.