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