At the end of the 1970s, the discovery of a catalytic RNA nestled in an intron, followed by another involved in the maturation of transfer RNAs, led to the discovery of new ribozymes and the transition from a strictly “proteocentric” vision, inherited from the dogma of molecular biology, to a more “nucleocentric” one. Since then, a variety of ribozymes have been identified in genomes, where their functions often remain mysterious.
Looking at Ribozymes traces the discovery of these molecules and presents a picture of their functional diversity, catalytic mechanisms and distribution within the tree of life.
Table of Contents
Foreword vii
Preface xi
Chapter 1 Fundamentals of RNA and Ribozyme Structure 1
1.1 Sequences and secondary structures 2
1.2 RNA folding, tertiary structures and 3D 8
1.2.1 Secondary structures and RNA folding 8
1.2.2 The pseudoknot 12
1.2.3 The loop E 14
1.2.4 The k-turn 16
1.2.5 Tetra-loop receptors 18
1.2.6 The A-minor pattern 20
1.2.7 Comparative analysis of sequences 24
Chapter 2 Ribozymes and the "Central Dogma" of Molecular Biology 29
2.1 The discovery of RNA catalysis and the central dogma of molecular biology 29
2.2 In search of the primordial polymerase 34
Chapter 3 The Discovery of Ribozymes 37
3.1 The discovery of catalysis by autocatalytic introns 38
3.2 The discovery of RNA catalysis of RNase P 42
3.3 The first consequences of these discoveries 46
3.3.1 The ribosome, a long-ignored ribozyme 47
3.3.2 The modified bases 52
3.4 The spliceosome, another ribozyme 55
3.4.1 Nucleolytic ribozymes 56
Chapter 4 Ribozyme Engineering and the RNA World 73
4.1 Classification of ribozymes 75
4.2 Classification of ribozymes according to catalytic mechanism 76
Chapter 5 Structures of Ribozymes 81
5.1 Structures and catalytic mechanisms of ribozymes 81
5.1.1 Hammerhead ribozymes 81
5.1.2 The example of the hairpin ribozyme 87
5.1.3 The example of the glmS ribozyme 89
5.2 An example of catalysis control: lariat-capping ribozyme 91
Chapter 6 Evolution of the Vision of the Catalytic Mechanisms of Ribozymes, the Hammerhead Ribozyme 99
6.1 Chemistry and catalysis: between general acid/base and metal cations 99
6.2 Difficulties in interpreting catalysis data 103
Chapter 7 The Distribution of Ribozymes in Living Organisms and Molecular Adaptations during Evolution 111
7.1 Ubiquitous ribozymes 111
7.2 Selection pressures at work in ribozyme shaping 113
7.3 Ribozymes in cellular processes: from viroids to eukaryotes 117
7.4 Very human ribozymes 123
Conclusion 133
References 135
Index 165
