Molecular Biology of RNA Processing and Decay in Prokaryotes (eBook)

Front Cover 1
Molecular Biology of RNA Processing and Decay in Prokaryotes 4
Copyright Page 5
Contents 6
Chapter 1: A Phylogenetic View of Bacterial Ribonucleases 10
I. Functions for Life 11
II. Ribonucleases of the Paleome 13
III. Ribonucleases of the Cenome 35
IV. Provisional Conclusion 39
Acknowledgments 41
References 41
Chapter 2: RNA Processing and Decay in Bacteriophage T4 52
I. Introduction 53
II. Part 1: Mechanisms and Regulation of mRNA Degradation During T4 Development 54
III. Part 2: Transfer RNA Processing 75
Acknowledgments 87
References 87
Chapter 3: Endonucleolytic Initiation of mRNA Decay in Escherichia coli 100
I. Background 101
II. General Features of mRNA Degradation in E. coli 106
III. Evidence for Diverse Pathways of mRNA Degradation in E. coli 111
IV. The Structure of RNase E 115
V. Substrate Specificity and Catalytic Mechanism of RNase E 121
VI. Modulators and Adaptors of RNase E 127
VII. Other Endoribonucleases in E. coli 128
VIII. Phylogenetic Distribution of RNase E and The RNA Degradosome 132
Acknowledgments 134
References 134
Chapter 4: Poly(A)-Assisted RNA Decay and Modulators of RNA Stability 146
I. Introduction 147
II. Regulation of Gene Expression in Response to Environmental Signals 148
III. Polyadenylation and Poly(A)-Dependent Decay 151
IV. Other Modulators of RNA Stability 167
V. Conclusions and Open Questions 176
References 178
Chapter 5: The Role of 3'-5' Exoribonucleases in RNA Degradation 196
I. Introduction 197
II. Polynucleotide Phosphorylase (PNPase) 202
III. RNase II 209
IV. RNase R 214
V. Oligoribonuclease 219
VI. Mechanisms of RNA Degradation 221
VII. Concluding Remarks 226
References 227
Chapter 6: Messenger RNA Decay and Maturation in Bacillus subtilis 240
I. Introduction and Historical Perspective 241
II. The 5' End 243
III. Body of The Message 260
IV. The 3' End 267
V. Regulated mRNA Decay 273
VI. Conclusion 276
References 276
Chapter 7: RNA Degradation in Archaea and Gram-Negative Bacteria Different from Escherichia coli 284
I. Introduction 285
II. RNA Degradation Mechanisms in Bacteria and Eukarya 286
III. Features of mRNA in Archaea 296
IV. Archaeal Proteins with Unexpected Endoribonucleolytic Activities 302
V. Archaeal Proteins with Similarities to Bacterial or Eukaryotic Proteins Involved in RNA Degradation - A Short Overview 308
VI. The Archaeal Exosome 309
VII. RNA Degradation in Archaea 317
VIII. Concluding Remarks 319
References 320
Chapter 8: The Making of tRNAs and More - RNase P and tRNase Z 328
I. Introduction 329
II. Processing by RNase P 333
III. Removal of the tRNA 3'-Trailer 356
Acknowledgments 367
References 367
Chapter 9: Maturation and Degradation of Ribosomal RNA in Bacteria 378
I. Introduction 378
II. Early Studies of rRNA Maturation and Degradation 379
III. Current Understanding of rRNA Processing 382
IV. Degradation of rRNA 392
Acknowledgments 397
References 397
Chapter 10: RNA Polyadenylation and Decay in Mitochondria and Chloroplasts 402
I. Introduction 403
II. Polyadenylation of RNA 404
III. The Enzymes 408
IV. RNA Degradation and Polyadenylation in Chloroplasts 417
V. RNA Degradation and Polyadenylation in Mitochondria 418
VI. Conclusions and Perspectives 422
Acknowledgments 423
References 423
Chapter 11: Killer and Protective Ribosomes 432
I. Introduction 433
II. Nucleolytic Versus Non-nucleolytic Inactivation of mRNAs 435
III. Translation-Degradation Interplay: Conceptual Ambiguities and Technical Caveats 439
IV. Killer Ribosomes 445
V. Protective Ribosomes 455
VI. Concluding Remarks 466
Acknowledgments 466
References 467
Chapter 12: mRNA Interferases, Sequence-Specific Endoribonucleases from the Toxin-Antitoxin Systems 476
I. Introduction 477
II. MazF: An mRNA Interferase 480
III. MazF Homologues and Other mRNA Interferases 489
IV. Other Toxins in TA Systems 498
V. The Regulation of MazF Expression Under Stress Conditions 500
VI. Concluding Remarks 503
Acknowledgments 504
References 505
Index 510