Progress in Nucleic Acid Research and Molecular Biology (eBook)

Cover 1
Contents 6
Abbreviations and Symbols 10
Some Articles Planned for Future Volumes 12
Chapter 1. Uracil Metabolism„UMP Synthesis from Orotic Acid or Uridine and Conversion of Uracil to ß-Alanine: Ennzymes and cDNAs 16
I. Overview of Pyrimidine Metabolism 17
II. Allosteric Regulation by Dissociation of Enzyme Oligomers 28
III. UMP Synthase2 33
IV. Uridine Kinase 55
V. ß-Alanine Synthase 64
VI. Enzyme Evolution 74
VII. Conclusion and Future Prospects 85
References 87
Chapter 2. The Importance of Being Modified: Roles of Modified Nucleosides and Mg2+ in RNA Structure and Function 94
I. Biological Functions of Modified Nucleosides 96
II. The large Array of Modified Ribonucleoside Structures and Chemistries 99
III. Site-selective Positioning of Modifications 116
IV. The Study of Modified-nucleoside Contributions to Structure and Function 120
V. Examples of Biophysical Contributions to Function by Modified Nucleosides 124
VI. Conclusions and Perspectives on the Importance of Being Modified 134
References 139
Chapter 3. Chemical and Computer Probing of RNA Structure 146
I. Probing RNA Structure by Chemical and Enzymatic Approaches 148
II. Computer Analysis of the Secondary Structure of RNA 179
III. Concluding Remarks 205
References 206
Chapter 4. Transcriptional Activation of Thymidine Kinase, a Marker for Cell Cycle Control 212
I. Major Players in the G0 to S Transition 213
II. Transcriptional Regulation of Thymidine Kinase as a Model for Late G1 Events 217
III. Role of E2F Complexes in the Mouse Thymidine Kinase Transcription 219
IV. Role of New Complexes Yi1 and Yi2 in the Mouse Thymidine Kinase Transcription 223
References 229
Chapter 5. Eukaryotic Gene Expression: Metabolite Control by Amino Acids 234
I. Amino-acid Control in Bacteria 234
II. Amino-acid Control in Yeast 235
III. Adaptive Regulation of Eukaryotic Plasma Membrane Amino-acid Transport 241
IV. Aminoacid-dependent Regulation of Asparagine Synthetase Expression 247
V. Identification and Characterization of Aminoacid-regulated Ribosomal-protein Genes 253
VI. Summary 260
References 260
Chapter 6. Molecular Recognition in the Assembly of the Segmented Reovirus Genome 264
I. Basic Features of the Reovirus Multiplication Cycle 267
II. The Nature of Reovirus Genome Segments 270
III. The Nature of Reovirus Defective Interfering Particles 274
IV. The Nature of Reovirus Genome Segment Reassortment and of the Reassortants That Are Generated 275
V. The Functions of Reovirus Proteins 276
VI. Reovirus Genome Segment Assortment Studied with Monoclonal Antibodies against Reovirus Proteins 284
VII. The Infectious Reovirus RNA System 285
VIII. The Interplay of Signals Required for the Insertion of Genetic Information into the Reovirus Genome 289
References 292
Chapter 7. Alu: Structure, Origin, Evolution, Significance, and Function of One-Tenth of Human DNA 298
I. Identifying and Defining Repetitive Sequence Families 300
II. Evolution of Alus (and Other Mammalian SINEs) 311
III. Genetic Effects of Alus and Other Repeats 316
IV. Does ALu Have a Function? 317
V. Prospectives and a Speculation 328
References 329
Chapter 8. Recent Advances in the Molecular Biology of Vitamin D Action 336
I. The Vitamin D Receptor 337
II. Vitamin D Receptor-DNA Interaction 340
III. Transcriptional Regulation Mechanism by Vitamin D 344
IV. The Molecular Biology of Vitamin D Hydroxylases 348
V. Summary 353
References 354
Chapter 9. Regulation of Synthesis of Ribonucleotide Reductase and Relationship to DNA Replication in Various Systems 360
I. Nature of Ribonucleotide Reductase Enzyme and Reaction 360
II. Time of Initiation of Bacteriophage T4 DNA Replication 364
III. Expression of T4 nrdA and nrdB Genes 366
IV. Expression of Escherichia coli nrdA and nrdB Genes 371
V. Phospholipid Synthesis and mRNA Breakdown Provide CMP for Synthesis of CDP and dCDP 374
VI. Control of Ribonucleotide Reductase Synthesis in Eukaryotes and Activity in Cell Division Cycle 376
VII. Effect of DNA Damage on nrdA and nrdB Expression 386
VIII. Ribonucleotide Reductase Regulation during Oogenesis 390
IX. Eukaryotic Animal DNA Viruses Encoding Ribonucleotide Reductases 394
X. Kinetics of Synthesis of T4-encoded Ribonucleotide Reductase and Relationship to T4 DNA Replication 398
XI. General Discussion 405
References 406
Index 412