Ribonuclease P (eBook)

Preface 4
I dedicate this preface to the memory of Hugh Robertson and the staff of the LMB whose unfailing commitment to training younger scientists, both directly and by example, have significantly contributed to the exceedingly productive careers of many influen 8
Contents 9
Contributors 11
1.1 RNase P and Life 15
1.2 The Initial Substrate 15
History of RNase P and Overview of Its Catalytic Activity 15
1.3 The Purification of RNase P 16
1.4 Diversion in Mammalian Cells 16
1.5 The Requirement for an RNA Component 17
1.6 Separation of Two Components 17
1.7 Reconstitution 18
1.8 Small Ribosome? 18
1.9 Catalytic Properties of RNA 19
1.10 Structure of RNase P 20
1.11 More Substrates 21
1.12 EGS Scheme 21
1.13 More EGS Experiments 22
1.14 Human RNase P 23
1.15 Reconstitution and Regulation of Human RNase P 24
1.16 An Overview of RNase P Research and our Current World 25
References 26
The Evolution of RNase P and Its RNA 30
2.1 Introduction 30
2.2 Bacterial Ribonuclease P 34
2.2.1 Bacterial RNase P RNA Structure Classes 35
2.2.2 Dimerization Mediated by the RNA 35
2.2.3 The Role of the Protein Subunit 36
2.2.4 RnpA is Part of a Conserved Genomic Arrangement 37
2.2.5 And Then There was One: Aquifex and the Missing Link 38
2.3 Archaeal Ribonuclease P 38
2.3.1 Archaeal RNase P RNA Structure Classes 39
2.3.2 Pyrococcus horikoshii OT3 as a Model For RNase P in Archaea 40
2.3.3 Two Flies in the Ointment: Nanoarchaeum and Pyrobaculum 42
2.4 Eukaryotic Ribonuclease P 43
2.4.1 Saccharomyces cerevisiae a Model for RNase P in Eukaryotes 43
2.5 Conclusion 48
References 49
Over a Decade of Bacterial Ribonuclease P Modeling 54
3.1 Introduction 54
3.1.1 Different Models 56
3.1.2 Different Approaches 57
3.1.3 Models as Answers to Biological Questions 58
3.2 Models in a Historical Perspective 58
3.3 Conclusions and Perspectives 69
References 71
Structural Studies of Ribonuclease P 76
4.1 Introduction 76
4.2 Structural Studies of Bacterial RNase P 77
4.2.1 Structures of the Protein Component 78
4.2.2 Structures of the S-Domain of Bacterial RNase P 79
4.2.3 Structures of the RNA Component of Bacterial RNase P 81
4.3 Structural Studies of Archaeal and Eukaryotic RNase P 84
4.4 Conclusions 87
References 87
Folding of Bacterial RNase P RNA 92
5.1 Introduction 92
5.2 Experimental Techniques and Data Analysis to Study P RNA Folding 93
5.3 Tertiary Structure of P RNA 95
5.4 Folding of the B-type, B. subtilis P RNA 96
5.5 Folding of the A-type, E. coli P RNA 98
5.6 P RNA Folding During Transcription 99
5.7 Future Directions and Questions for P RNA Folding 102
References 103
Kinetic Mechanism of Bacterial RNase P 105
6.1 Introduction 105
6.2 P RNA Coordinates a Metal-Hydroxyl That Functions as a Nucleophile to Catalyze Hydrolysis of the Scissile Phosphate 107
6.3 A Minimal Kinetic Scheme for RNase P 110
6.4 Contributions of P Protein to RNase P Function 114
6.5 Metal-Ion Association with Bacterial RNase P Holoenzyme 115
6.6 Isomerization in the Kinetic Mechanism of RNase P 117
6.7 Conclusions and Further Questions 118
References 118
Roles of Metal Ions in RNase P Catalysis 124
7.1 Introduction 124
7.2 Identification of Metal(II)-Ion Binding Sites 126
7.3 Different Metal(II)-Ions and RNase P RNA 129
7.4 Metal(II)-Ions and the RNase P Protein 131
7.5 Metal(II)-Ions, Substrate Interaction and Cleavage 131
7.5.1 The TSL-/TBS Interaction 132
7.5.2 The RCCA–RNase P RNA Interaction 133
7.5.3 The A 134
7.5.4 The U 134
7.6 Orchestration of the Cleavage Site and Cleavage 135
7.7 RNase P RNA, Antibiotics and “Metal Mimics” 139
References 140
Challenges in RNase P Substrate Recognition: Considering the Biological Context 146
8.1 Introduction 146
8.2 Contribution of RNase P Processing to the Overall Rate of tRNA Biosynthesis 147
8.3 The Power (and limitations) of the “Reductionist” Perspective on RNase P Substrate Recognition 151
8.4 Facing up to the Biological Context 155
8.5 Summary and Perspective 160
References 161
Archaeal RNase P: A Mosaic of Its Bacterial and Eukaryal Relatives 163
9.1 Introduction 163
9.2 Isolation and Characterization of Native Archaeal RNase P Holoenzymes 164
9.3 Archaeal RNase P RNA (RPR) 165
9.4 Archaeal RNase P Proteins (RPPs) 170
9.5 Pyrobaculum RNase P Exemplifies the Extraordinary Divergence in Thermoproteaceae 176
9.6 Concluding Remarks 177
References 179
Eukaryote RNase P and RNase MRP 183
10.1 Introduction: Increased Complexity in the Eukaryote 183
10.2 Multiple RNase P Enzymes Exist in Eukaryotes 184
10.2.1 Yeast Nuclear RNase P 184
10.2.2 Mitochondrial RNase P 186
10.2.3 Yeast RNase MRP 186
10.2.4 Comparison with the Human Enzymes 188
10.3 Substrate Specificity and Mechanism 190
10.3.1 RNase P Mechanism 191
10.3.2 RNase P Substrate Specificity 191
10.3.3 RNase MRP Substrate Specificity 193
10.4 The Eukaryote RNA Subunits 194
10.5 The Protein Subunits: Holoenzyme Architecture 200
10.5.1 Holoenzyme Assembly (in Vivo) 201
10.5.2 RNA–Protein Interactions 202
10.5.3 Protein–Protein Interactions 203
10.6 Perspective 205
References 205
RNase P from Organelles 213
11.1 Introduction 213
11.2 Mitochondria 214
11.2.1 Yeast Mitochondria 214
11.2.2 Other Fungi 218
11.2.3 Plant Mitochondria 219
11.2.4 Other Organisms with Bacterial-Like Mitochondrial P RNA 220
11.2.5 Trypanosomatids 221
11.2.6 Human Mitochondria 221
11.3 Plastids 223
References 229
Human RNase P and Transcription 233
12.1 Characterization of a Human RNase P Ribonucleoprotein 233
12.2 A Role for Human RNase P Ribonucleoprotein in Transcription by Pol III 235
12.3 A Novel Role for Human RNase P in rDNA Transcription by Pol I 236
12.4 Recruitment and Assembly of RNase P on Chromatin of Target Genes 237
12.5 What Is the Exact Role of RNase P in Transcription? 239
12.6 Does RNase P Affect Pol II Transcription? 239
12.7 RNase P in Regulation of Expression of Noncoding RNA 240
12.8 Prospects 241
References 241
RNase P as a Drug Target 245
13.1 Introduction 245
13.2 Antisense Inhibitors 247
13.3 Aminoglycosides and Arginine Derivatives 252
13.4 Structure-Based Drug Design Using the Bacterial P Protein as Target 256
13.5 Inhibitors of RNase P from Eukaryotic Pathogens 257
13.6 Other Small Ligand Effectors 13.6.1 Synthetic Inhibitors Which Act by Binding to the Substrate 261
13.6.2 Macrolides as Activators of Bacterial RNase P 263
13.7 Final Remarks 263
References 264
Ribonuclease P as a Tool 267
14.1 Introduction 267
14.2 Gene Targeting Strategy Based on RNase P 268
14.3 In Vitro Characterization of RNase P-Mediated Targeting Approaches 270
14.4 Characterization of RNase P-Mediated Approaches in Cultured Cells 272
14.5 Engineering of EGS and M1GS RNAs by In Vitro Selection 274
14.5.1 In Vitro Selection of M1GS RNAs 274
14.5.2 In Vitro Selection of EGSs 275
14.6 Characterization of RNase P Targeting in Animals 276
14.7 Applications of RNase P as a Tool for Basic Research and for Therapy 276
14.8 Advantage and Disadvantage of M1GS and RNase P-EGS Technology 279
14.9 Conclusion 281
References 281
Index 286