Maximizing Gene Expression

Preface
1. E. Coli Promoters
1.1 Defining Promoters
1.2 Structure Analysis
1.3 Steps in Transcription Initiation
1.4 Structure-Function Correlation
1.5 Regulation of Transcription Initiation
1.6 Conclusion
References
2. Yeast Promoters
2.1 Transcription in Yeast
2.2 Methods for Studying Yeast Promoters
2.3 Upstream Promoter Elements
2.4 The TATA Promoter Element
2.5 Elements that Select Initiation Sites
2.6 Transcription Regulation
2.7 Regulatory Proteins
2.8 Other Aspects of Regulation
2.9 Complex Promoter Organization
2.10 Molecular Mechanisms: Inferences and Speculations
References
3. Protein Coding Genes of Higher Eukaryotes: Promoter Elements and trans-Acting Factors
3.1 The TATA Box and the Cap Site
3.2 The Upstream Promoter Elements
3.3 Enhancer Elements
3.4 Other trans-Kcúng Factors
3.5 Conclusion and Prospects
References
4. The Instability of Messenger RNA in Bacteria
4.1 Some Fundamental Observations and Their Significance
4.2 Mechanistic Models
4.3 Search for Specific Enzymes for mRNA Degradation
4.4 The Search for Targets
4.5 Searching for New Ends
4.6 Searching for a Model
4.7 Conclusions
References
5. Replication Control of the ColE1-Type Plasmids
5.1 Incompatibility
5.2 Replication of ColE1 DNA In Vitro
5.3 RNA I and Primer Processing
5.4 RNA I Secondary Structure
5.5 Mutations in RNA I and Primer That Define Domains of Interaction
5.6 Analysis of the RNA I-Primer Interaction
5.7 The Replication Primer
5.8 Replication-Defective Mutants
5.9 Temperature-Sensitive Replication Mutants
5.10 The rop Function
5.11 Partition and Stability Functions
5.12 Host Contributions to ColE1 Replication
5.13 On the Control of the Control Elements
5.14 Implications for Maximizing Gene Expression
References
6. Copy Number and Stability of Yeast Plasmids
6.1 Vectors for DNA Cloning in Saccharomyces Cerevisiae
6.2 Elements of the 2µ Circle Replication System
6.3 Factors Affecting the Stability and Copy Number of Hybrid 2µ-Based Plasmids
6.4 Conclusion
References
7. Translation Initiation
7.1 Prokaryotes
7.2 Eukaryotes
7.3 Conclusion
References
8. Biased Codon Usage: An Exploration of Its Role in Optimization of Translation
8.1 Codon Usage
8.2 Physiological Aspects of Codon Usage
8.3 Codon Context and tRNA-tRNA Interaction
8.4 Evolutionary Aspects of Codon Usage
8.5 Altering Codon Bias Experimentally
References
9. The Selective Degradation of Abnormal Proteins in Bacteria
9.1 Proteins Rapidly Hydrolyzed in E. Coli
9.2 Intracellular Aggregates of Abnormal Polypeptides
9.3 The Energy Requirement and Pathway for Protein Breakdown
9.4 ATP-Stimulated Proteolysis in Cell-Free Extracts
9.5 Proteolytic Enzymes in E. Coli
9.6 Protease La, the ATP-Dependent Protease
9.7 The ATP-Dependent Proteolytic Mechanism
9.8 Regulation of Ion Expression
9.9 Protein Breakdown and the Heat Shock Response
9.10 Unanswered Questions
References
10. Detection of Proteins Produced by Recombinant DNA Techniques
10.1 Complementation of E. Coli Mutants
10.2 Complementation of Yeast Mutants
10.3 Complementation in Mammalian Cells
10.4 Rescue of the Sequence Conferring the New Phenotype
10.5 Complementation in Drosophila
10.6 Detection Using Immunological Methods
10.7 Detection Using Antisera Raised Against Synthetic Peptides
References 338
11. Mechanism and Practice
11.1 Transcription Initiation
11.2 Translation Initiation
11.3 Messenger Stability and Secondary Structure
11.4 Gene Amplification
11.5 Protein Stability
References
Index