Liu / Altman Ribonuclease P

1. Auflage 2009
ISBN: 978-1-4419-1142-1
Verlag: Springer
Format: PDF
Kopierschutz: 1 - PDF Watermark

E-Book, Englisch, Band 10, 283 Seiten

Reihe: Protein Reviews

The Discovery of Ribonuclease P and Enzymatic Activity of Its RNA Subunit Sydney Brenner and Francis H. C. Crick had a specific project in mind when they offered Sidney Altman a position in their group in 1969 to conduct postdoctoral research at the Medical Research Council Laboratory of Molecular Biology (LMB) in Cambridge, England. At the time, an intense international competition was on- ing in as many as a dozen labs to determine the three-dimensional structure of tRNA. At the LMB, Aaron Klug was attacking the structure by crystallographic analysis with Brian F. C. Clark providing large amounts of purified phenylalanine tRNA. (Eventually, Aaron announced his empirically determined 3-D structure of yeast phenylalanine tRNA, a structure that is generally common to tRNAs, due in part to several conserved, novel three-way nucleotide interactions. ) Concurrently, Michael Levitt, a Ph. D. student of Francis, was visually scrutinizing the cloverleaf secondary structure of the 14 tRNA sequences known at the time. Levitt was searching for nucleotide covariation in different parts of the molecules that were conserved in the 14 sequences known at the time. He identified a possible covariation of an apparent Watson-Crick pairing type between the residues at position 15 from the 5' end of the tRNA and residue 48. This association implied these parts of the tRNA, namely the D loop containing residue 15 and the 5' end of the T stem-adjoining residue 48, folded on one another in a tertiary structure shared by different tRNAs.

Autoren/Hrsg.

Liu, Fenyong

Altman, Sidney

Inhaltsverzeichnis

1;Preface;4
1.1;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
2;Contents;9
3;Contributors;11
3.1;1.1 RNase P and Life;15
3.2;1.2 The Initial Substrate;15
4;History of RNase P and Overview of Its Catalytic Activity;15
4.1;1.3 The Purification of RNase P;16
4.2;1.4 Diversion in Mammalian Cells;16
4.3;1.5 The Requirement for an RNA Component;17
4.4;1.6 Separation of Two Components;17
4.5;1.7 Reconstitution;18
4.6;1.8 Small Ribosome?;18
4.7;1.9 Catalytic Properties of RNA;19
4.8;1.10 Structure of RNase P;20
4.9;1.11 More Substrates;21
4.10;1.12 EGS Scheme;21
4.11;1.13 More EGS Experiments;22
4.12;1.14 Human RNase P;23
4.13;1.15 Reconstitution and Regulation of Human RNase P;24
4.14;1.16 An Overview of RNase P Research and our Current World;25
4.15;References;26
5;The Evolution of RNase P and Its RNA;30
5.1;2.1 Introduction;30
5.2;2.2 Bacterial Ribonuclease P;34
5.2.1;2.2.1 Bacterial RNase P RNA Structure Classes;35
5.2.2;2.2.2 Dimerization Mediated by the RNA;35
5.2.3;2.2.3 The Role of the Protein Subunit;36
5.2.4;2.2.4 RnpA is Part of a Conserved Genomic Arrangement;37
5.2.5;2.2.5 And Then There was One: Aquifex and the Missing Link;38
5.3;2.3 Archaeal Ribonuclease P;38
5.3.1;2.3.1 Archaeal RNase P RNA Structure Classes;39
5.3.2;2.3.2 Pyrococcus horikoshii OT3 as a Model For RNase P in Archaea;40
5.3.3;2.3.3 Two Flies in the Ointment: Nanoarchaeum and Pyrobaculum;42
5.4;2.4 Eukaryotic Ribonuclease P;43
5.5;2.4.1 Saccharomyces cerevisiae a Model for RNase P in Eukaryotes;43
5.6;2.5 Conclusion;48
5.7;References;49
6;Over a Decade of Bacterial Ribonuclease P Modeling;54
6.1;3.1 Introduction;54
6.1.1;3.1.1 Different Models;56
6.1.2;3.1.2 Different Approaches;57
6.1.3;3.1.3 Models as Answers to Biological Questions;58
6.2;3.2 Models in a Historical Perspective;58
6.3;3.3 Conclusions and Perspectives;69
6.4;References;71
7;Structural Studies of Ribonuclease P;76
7.1;4.1 Introduction;76
7.2;4.2 Structural Studies of Bacterial RNase P;77
7.2.1;4.2.1 Structures of the Protein Component;78
7.2.2;4.2.2 Structures of the S-Domain of Bacterial RNase P;79
7.2.3;4.2.3 Structures of the RNA Component of Bacterial RNase P;81
7.3;4.3 Structural Studies of Archaeal and Eukaryotic RNase P;84
7.4;4.4 Conclusions;87
7.5;References;87
8;Folding of Bacterial RNase P RNA;92
8.1;5.1 Introduction;92
8.2;5.2 Experimental Techniques and Data Analysis to Study P RNA Folding;93
8.3;5.3 Tertiary Structure of P RNA;95
8.4;5.4 Folding of the B-type, B. subtilis P RNA;96
8.5;5.5 Folding of the A-type, E. coli P RNA;98
8.6;5.6 P RNA Folding During Transcription;99
8.7;5.7 Future Directions and Questions for P RNA Folding;102
8.8;References;103
9;Kinetic Mechanism of Bacterial RNase P;105
9.1;6.1 Introduction;105
9.2;6.2 P RNA Coordinates a Metal-Hydroxyl That Functions as a Nucleophile to Catalyze Hydrolysis of the Scissile Phosphate;107
9.3;6.3 A Minimal Kinetic Scheme for RNase P;110
9.4;6.4 Contributions of P Protein to RNase P Function;114
9.5;6.5 Metal-Ion Association with Bacterial RNase P Holoenzyme;115
9.6;6.6 Isomerization in the Kinetic Mechanism of RNase P;117
9.7;6.7 Conclusions and Further Questions;118
9.8;References;118
10;Roles of Metal Ions in RNase P Catalysis;124
10.1;7.1 Introduction;124
10.2;7.2 Identification of Metal(II)-Ion Binding Sites;126
10.3;7.3 Different Metal(II)-Ions and RNase P RNA;129
10.4;7.4 Metal(II)-Ions and the RNase P Protein;131
10.5;7.5 Metal(II)-Ions, Substrate Interaction and Cleavage;131
10.5.1;7.5.1 The TSL-/TBS Interaction;132
10.5.2;7.5.2 The RCCA–RNase P RNA Interaction;133
10.5.3;7.5.3 The A;134
10.5.4;7.5.4 The U;134
10.6;7.6 Orchestration of the Cleavage Site and Cleavage;135
10.7;7.7 RNase P RNA, Antibiotics and “Metal Mimics”;139
10.8;References;140
11;Challenges in RNase P Substrate Recognition: Considering the Biological Context;146
11.1;8.1 Introduction;146
11.2;8.2 Contribution of RNase P Processing to the Overall Rate of tRNA Biosynthesis;147
11.3;8.3 The Power (and limitations) of the “Reductionist” Perspective on RNase P Substrate Recognition;151
11.4;8.4 Facing up to the Biological Context;155
11.5;8.5 Summary and Perspective;160
11.6;References;161
12;Archaeal RNase P: A Mosaic of Its Bacterial and Eukaryal Relatives;163
12.1;9.1 Introduction;163
12.2;9.2 Isolation and Characterization of Native Archaeal RNase P Holoenzymes;164
12.3;9.3 Archaeal RNase P RNA (RPR) ;165
12.4;9.4 Archaeal RNase P Proteins (RPPs) ;170
12.5;9.5 Pyrobaculum RNase P Exemplifies the Extraordinary Divergence in Thermoproteaceae;176
12.6;9.6 Concluding Remarks;177
12.7;References;179
13;Eukaryote RNase P and RNase MRP;183
13.1;10.1 Introduction: Increased Complexity in the Eukaryote;183
13.2;10.2 Multiple RNase P Enzymes Exist in Eukaryotes;184
13.2.1;10.2.1 Yeast Nuclear RNase P;184
13.2.2;10.2.2 Mitochondrial RNase P;186
13.2.3;10.2.3 Yeast RNase MRP;186
13.2.4;10.2.4 Comparison with the Human Enzymes;188
13.3;10.3 Substrate Specificity and Mechanism;190
13.3.1;10.3.1 RNase P Mechanism;191
13.3.2;10.3.2 RNase P Substrate Specificity;191
13.3.3;10.3.3 RNase MRP Substrate Specificity;193
13.4;10.4 The Eukaryote RNA Subunits ;194
13.5;10.5 The Protein Subunits: Holoenzyme Architecture;200
13.5.1;10.5.1 Holoenzyme Assembly (in Vivo);201
13.5.2;10.5.2 RNA–Protein Interactions;202
13.5.3;10.5.3 Protein–Protein Interactions;203
13.6;10.6 Perspective;205
13.7;References;205
14;RNase P from Organelles;213
14.1;11.1 Introduction;213
14.2;11.2 Mitochondria;214
14.2.1;11.2.1 Yeast Mitochondria;214
14.2.2;11.2.2 Other Fungi;218
14.2.3;11.2.3 Plant Mitochondria;219
14.2.4;11.2.4 Other Organisms with Bacterial-Like Mitochondrial P RNA;220
14.2.5;11.2.5 Trypanosomatids;221
14.2.6;11.2.6 Human Mitochondria;221
14.3;11.3 Plastids;223
14.4;References;229
15;Human RNase P and Transcription;233
15.1;12.1 Characterization of a Human RNase P Ribonucleoprotein;233
15.2;12.2 A Role for Human RNase P Ribonucleoprotein in Transcription by Pol III;235
15.3;12.3 A Novel Role for Human RNase P in rDNA Transcription by Pol I;236
15.4;12.4 Recruitment and Assembly of RNase P on Chromatin of Target Genes;237
15.5;12.5 What Is the Exact Role of RNase P in Transcription?;239
15.6;12.6 Does RNase P Affect Pol II Transcription?;239
15.7;12.7 RNase P in Regulation of Expression of Noncoding RNA;240
15.8;12.8 Prospects;241
15.9;References;241
16;RNase P as a Drug Target;245
16.1;13.1 Introduction;245
16.2;13.2 Antisense Inhibitors;247
16.3;13.3 Aminoglycosides and Arginine Derivatives;252
16.4;13.4 Structure-Based Drug Design Using the Bacterial P Protein as Target;256
16.5;13.5 Inhibitors of RNase P from Eukaryotic Pathogens;257
16.6;13.6 Other Small Ligand Effectors 13.6.1 Synthetic Inhibitors Which Act by Binding to the Substrate;261
16.7;13.6.2 Macrolides as Activators of Bacterial RNase P;263
16.8;13.7 Final Remarks;263
16.9;References;264
17;Ribonuclease P as a Tool;267
17.1;14.1 Introduction;267
17.2;14.2 Gene Targeting Strategy Based on RNase P;268
17.3;14.3 In Vitro Characterization of RNase P-Mediated Targeting Approaches ;270
17.4;14.4 Characterization of RNase P-Mediated Approaches in Cultured Cells;272
17.5;14.5 Engineering of EGS and M1GS RNAs by In Vitro Selection;274
17.5.1;14.5.1 In Vitro Selection of M1GS RNAs;274
17.5.2;14.5.2 In Vitro Selection of EGSs;275
17.6;14.6 Characterization of RNase P Targeting in Animals;276
17.7;14.7 Applications of RNase P as a Tool for Basic Research and for Therapy;276
17.8;14.8 Advantage and Disadvantage of M1GS and RNase P-EGS Technology ;279
17.9;14.9 Conclusion;281
17.10;References;281
18;Index;286