Translational Regulation of Gene Expression

1 Translational Regulation of Ribosomal Proteins in Escherichia coli: Molecular Mechanisms.- 1. Evidence for Autoregulation of Ribosomal Proteins.- 2. Regulation of the ? Operon by S4.- 2.1. Introduction.- 2.2. Thermodynamics of S4-Messenger RNA Complex Formation.- 2.3. Structure of the ? Messenger RNA Leader.- 3. Regulation of the L11 Operon by L1.- 4. Regulation of the rif Operon by L10.- 5. Other Ribosomal-Protein Repressors.- 6. Common Themes in Ribosomal-Protein Autoregulation.- 7. Thermodynamics of Translational Repression.- 7.1. Thermodynamics of Translation.- 7.2. Translation and Repression In Vivo.- 8. Predictions of Different Translational Repression Models.- 8.1. Displacement Model.- 8.2. Entrapment Model.- 8.3. Influences of Protein Binding on Messenger RNA Turnover...- 8.4. Prediction of Gene-Dosage Effects.- 9. Influence of Messenger RNA Secondary Structure on Translation...- 10. Future Directions.- References.- 2 Translational Regulation in Bacteriophages.- 1. Introduction.- 2. RNA Phage.- 2.1. Repression by Replicase.- 2.2. Repression by Coat Protein.- 3. T4 Gene 32.- 3.1. Autogenous Translational Repression.- 3.2. Binding Parameters.- 3.3. Quantitative Model of Repression.- 3.4. Tests of the Model.- 4. f1 Gene V.- 5. P22 Gene 8.- 6. T4 RegA Protein.- 7. Structural Repression and Activation.- 8. Conclusions.- References.- 3 Escherichia coli Threonyl-Transfer RNA Synthetase as a Model System to Study Translational Autoregulation in Prokaryotes.- 1. Introduction.- 2. Structure of the Escherichia coli Genome around the Gene for Threonyl-Transfer RNA Synthetase.- 3. The Expression of the Gene for Threonyl-Transfer RNA Synthetase Is Negatively Autoregulated at the Translational Level.- 3.1. In Vitro Studies.- 3.2. In Vivo Studies.- 4. Genetic Definition of the Translational Operator.- 4.1. Isolation of Operator Constitutive Mutants.- 4.2. Nucleotide Sequence of the Operator Constitutive Mutants.- 4.3. Homologies between the thrS Translational Operator and the Threonine-Specific Transfer RNAs.- References.- 4 Translational Regulation of Ribosomal Protein Gene Expression in Eukaryotes.- 1. Introduction.- 2. Translational Regulation of Yeast Ribosomal Protein Synthesis.- 2.1. Genetics of Yeast Ribosomal Proteins.- 2.2. Is There Life after Transcription?.- 2.3. Evidence for Translational Regulation of Yeast Ribosomal Protein Synthesis.- 2.4. Other Aspects of Ribosomal Protein Messenger RNA Translation.- 2.5. Future Directions.- 3. Translational Regulation of Ribosomal Protein Synthesis during Drosophila Development.- 4. Translational Regulation of Ribosomal Protein Synthesis during Xenopus Development.- 5. Translational Regulation of Ribosomal Protein Synthesis during Mammalian Development.- 6. Translational Regulation of Ribosomal Protein Synthesis in Other Eukaryotic Cells.- 7. Conclusions and Prospects.- References.- 5 Selective Messenger RNA Translation in Marine Invertebrate Oocytes, Eggs, and Zygotes.- 1. Introduction.- 2. Translational Control in Sea Urchin Eggs and Embryos.- 2.1. Role of Changes in the Translational Machinery.- 2.2. Role of Changes in the Availability of Messenger RNA.- 3. Quantitative Changes in Other Organisms.- 3.1. Qualitative Changes in Protein Synthesis.- 3.2. Mechanisms of Selective Translation.- 3.3. Regulation of Message Availability through the Association of the Maternal Messenger RNA with Other Macromolecules.- 3.4. Changes in Messenger RNA Structure Related to Changes in the Translation of Different Messenger RNAs.- 3.5. Role of Messenger RNA Competition in Changing Relative Rates of Messenger RNA Utilization.- 3.6. Role of Messenger RNA Localization in Selective Translation 104 4. Conclusions.- References.- 6 Molecular Mechanisms of Translational Control during the Early Development of Xenopus laevis.- 1. Introduction.- 2. Oogenesis and Embryogenesis in Xenopus laevis.- 2.1. RNA and Protein Synthesis during Oogenesis.- 2.2. Messenger RNA Recruitment during Oocyte Maturation.- 2.3. Messenger RNA Recruitment during Embryogenesis.- 3. Compartmentalization of Messenger RNAs.- 3.1. Localized Messenger RN As.- 3.2. Membrane-Bound Messenger RNAs.- 4. Special Features of Translational Control.- 4.1. Translational Capacity of Oocytes.- 4.2. RNA Binding Proteins.- 4.3. Interspersed RNAs.- 4.4. Heat-Shock Response.- 4.5 Role of Polyadenylation.- 5. Conclusions.- References.- 7 Storage and Translation of Ferritin Messenger RNA.- 1. Introduction.- 2. Ferritin Structure.- 2.1. Protein Shell.- 2.2. Iron Core and Iron-Protein Interactions.- 3. Storage of Ferritin Messenger RNA.- 3.1. Ferritin Messenger RNA Encoding a Luxury Protein.- 3.2. Ferritin Messenger RNA Encoding a Housekeeping Protein.- 3.3. Significance of Ferritin Messenger RNA Storage.- 4. Translational Efficiency of Ferritin Messenger RNA.- 4.1. Translational Competition in Whole Cells.- 4.2. Translational Competition in Cell-Free Systems.- 4.3. Ferritin Messenger RNA Structure.- 5. Ferritin Gene Organization.- 6. Summary and Conclusions.- References.- 8 Regulation of Messenger RNA Translation at the Elongation Step during Estradiol-Induced Vitellogenin Synthesis in Avian Liver.- 1. Introduction.- 2. Analysis of Polypeptide Chain Elongation in Eukaryotic Systems.- 2.1. Examples of Gene Regulation at the Level of Polypeptide Chain Elongation.- 2.2. Methods of Analyzing Rates of Polypeptide Chain Elongation.- 2.3. Polypeptide Chain Elongation in Cockerel Liver following 17?- Estradiol Stimulation: Analysis of the Average Rate and of Specific Rates for Serum Albumin and Vitellogenin Peptides.- 3. Mechanisms of Regulation at the Elongation Step of Protein Synthesis.- 4. Concluding Remarks.- References.- 9 Translational Regulation in the Heat-Shock Response of Drosophila Cells.- 1. Introduction.- 2. Background.- 2.1. Heat-Shock Proteins..- 2.2. General Features of the Drosophila Response.- 3. Translational Specificity during Heat Shock.- 3.1. General Description of the Change in Translational Specificity.- 3.2. Models of Regulation.- 3.3. Heat-Shock Message-Translation Element.- 3.4. What Cellular Component Discriminates among Messages?.- 4. Translational Regulation during Recovery.- 4.1 Characterization of the Recovery Process.- 4.2. Possible Mechanisms of Recovery.- 5. Conclusions.- References.- 10 Strategies of Fibroin Production.- 1. Introduction.- 2. Fibroin-Synthesizing Systems.- 2.1. Bombyx mori.- 2.2. Spiders.- 3. Nephila clavipes Model System.- 3.1. Large Ampullate Glands.- 3.2. Cell-Free Translation.- 3.3. Discontinuous Translation.- 3.4. Transfer RNA Functional Adaptation.- 4. Alanine Transfer RNA Isoacceptors.- 5. Alanine Transfer RNA Genes in Bombyx mori.- 6. Relevance to the Nephila System.- References.- 11 Translational Regulation during Photomorphogenesis.- 1. Overview.- 2. Translational Regulation Accompanying Chloroplast Biogenesis.- 3. Translational Regulation Accompanying Cytodifferentiation in Volvox.- 4. Future Studies.- References.- 12 Gene Expression in Muscle: The Role of Small RNAs in the Expression of Muscle-Specific Proteins.- 1. Introduction.- 2. Interaction of Translational Control RNA102 with Messenger RNAs.- 2.1. Interaction In Vivo.- 2.2. Interaction In Vitro.- 2.3. Sequence Homology between Myosin Heavy-Chain Messenger RNA and Translational Control RNA102.- 3. Identification of a Translational Control RNA102 Gene.- 4. Subspecies of Translational Control RNA102.- 5. Conclusion and Prospects.- References.- 13 Involvement of Nucleotides in Protein Synthesis Initiation.- 1. Introduction.- 2. Requirement for GTP: Eukaryotic Initiation Factor 2.- 3. Other GTP Binding Proteins: Eukaryotic Initiation Factor 5.- 4. GTP Binding Domain.- 5. Requirement for ATP: Messenger RNA Binding.- 5.1. Eukaryotic Initiation Factor 4A.- 5.2. Eukaryotic Initiation Factor 4F.- 6. Interaction of the Messenger RNA Specific Factors.- 7. Mechanism of Binding Messenger RNA.- 8. Control of Protein Synthesis by Nucleotide Binding Proteins.- References.- 14 Roles of Eukaryotic Initiation Factor 2 and Eukaryotic Initiation Factor 2 Ancillary Protein Factors in Eukaryotic Protein Synthesis Initiation.- 1. Introduction.- 2. Roles of Eukaryotic Initiation Factor 2 and Eukaryotic Initiation Factor 2 Ancillary Protein Factors in Regulation of Protein Synthesis Initiation.- 2.1. Animal Cells.- 2.2. Lower Eukaryotic Cells.- 3. Concluding Remarks.- References.- 15 Role of Eukaryotic Messenger RNA Cap-Binding Protein in Regulation of Translation.- 1. Introduction.- 2. Cap-Binding Proteins Involved in Translation Initiation.- 2.1. Early Studies.- 2.2. ATP-Dependent Cap-Binding Proteins.- 2.3. Inactivation of Cap-Binding Protein Function after Poliovirus Infection and the Discovery of a New Initiation Factor.- 2.4. Structural Analysis of Cap-Binding Proteins and Their Subcellular Distribution.- 3. Messenger RNA Secondary Structure and Cap Recognition.- 3.1. Introduction.- 3.2. ATP and Cap Recognition.- 3.3. Ionic Strength and Cap Function.- 3.4. Poliovirus Infection and Cap-Binding Protein Activity.- 4. Discriminatory Activity of the Cap-Binding Protein Complex.- 5. Role of Cap-Binding Proteins in Regulation of Gene Expression.- 5.1. Poliovirus Infection of HeLa Cells.- 5.2. Heat Shock.- 5.3. Involvement of the Cap Structure in Control of Gene Expression in Other Systems.- 6. Concluding Remarks.- References.- 16 Differential Translation of Eukaryotic Messenger RNAs: The Role of Messenger RNA Secondary Structure.- 1. Introduction.- 2. Examples of Translational Regulation Mediated through Differential Messenger RNA Translational Efficiencies.- 3. Experimental Analysis of Messenger RNA Secondary Structure.- 4. Analysis of the Cleavage Patterns.- 5. Conclusion.- References.- 17 Translational and Nontranslational Mechanisms of Regulation by Eukaryotic Suppressor Mutants.- 1. Introduction.- 2. Suppressor Mechanisms.- 3. Transcriptional Regulation.- 4. Translational Regulation.- 5. Posttranslational Regulation.- 5.1. Vermilion Mutant.- 5.2. Suppression of Vermilion and Tryptophan Oxygenase.- 5.3. Purple Mutant.- 5.4. Suppression of Purple and 6-Pyruvoyltetrahydropterin Synthase.- 5.5. Suppression of Speck and Phenol Oxidase.- 6. Summary..- References.- 18 Translational Control of a Transcriptional Activator in the Regulation of Amino Acid Biosynthesis in Yeast.- 1. Introduction.- 2. General Amino Acid Control.- 3. cis-Acting Transcriptional Signals in General Amino Acid Control.- 4. A Hierarchy of trans-Acting Regulatory Factors in the General Amino Acid Control.- 5. Translational Control of GCN4 Expression.- 6. Translational Control of GCN4 Is Mediated by Multiple Upstream AUG Codons in GCN4 Messenger RNA.- 7. Functional Differentiation of the Upstream AUG Codons in GCN4 Messenger RNA.- 8. Translational Control of GCN4 and the Scanning Hypothesis.- References.- 19 The Role of Messenger RNA Sequences and Structures in Eukaryotic Translation.- 1. Introduction.- 2. An AUG Codon Is Required for Efficient Initiation of Translation.- 3. Effects of AUG Context on Translation.- 4. Sequences Adjacent to the AUG Initiation Codon and Effects of the Length of the Leader Region.- 5. Effects of Messenger RNA Secondary Structures and Sequences That Diminish Translation.- 6. Initiation Codon Selection.- 7. Eukaryotic Ribosomes Can Terminate and Then Reinitiate Translation.- 8. Polycistronic Messenger RNA in Eukaryotes.- 9. Translational Control and AUG Selection.- 10. Concluding Remarks.- References.- 20 Translational Regulation by Adenovirus Virus-Associated I RNA.- 1. Adenovirus Group.- 2. Organization of the Adenovirus Genome.- 3. Adenovirus Virus-Associated RNAs.- 4. Translational Alterations in Adenovirus-Infected Cells.- 5. Virus-Associated I RNA Is Required for Translation in Late Adenovirus-Infected Cells.- 6. Virus-Associated I RNA Is Required for Translation Initiation in Late Adenovirus-Infected Cells.- 7. Function of Virus-Associated I RNA.- 7.1. Regulation of Translation—An Overview.- 7.2. Eukaryotic Initiation Factor 2 Is Inactive in dl331 (VAI —)- Infected Cells.- 7.3. Interferon-Induced Pl/eIF-2 ?-Kinase Is Active in dl331- Infected Cells.- 7.4. Virus-Associated I RNA Prevents Activation of the Pl/eIF-2 ? -Kinase.- 7.5. Structural Requirements for Virus-Associated I RNA Function.- 8. Mechanism of Virus-Associated I RNA Activity.- 9. Other Viral Translation Regulation Mechanisms.- References.- 21 Translational Control of Transcription Termination in Prokaryotes.- 1. Introduction.- 2. Transcription Termination and RNA Polymerase Pausing.- 2.1. Rho-Independent Transcription Termination.- 2.2. Rho-Dependent Transcription Termination.- 3. Translational Control of Transcription Termination: Attenuation.- 3.1. General Features of Attenuator Control of Amino Acid Biosynthetic Opérons.- 3.2. Attenuation Control of the ilvGMEDA Operon of the Isoleucine-Valine Regulon of Escherichia coli K-12.- 3.3. Attenuation Control of the ?-Lactamase Gene of Escherichia coli.- 3.4. Attenuation Control of the Aspartate Transcarbamoylase (pyrBI) Operon.- 3.5. Attenuation Control of the Phenylalanyl-Transfer RNA Synthetase (pheST) Operon.- 3.6. Translational Control of the Erythromycin Resistance Gene.- 3.7. Attenuation Control of the Tryptophanase (tna) Operon.- References.