HDV Family of Self-Cleaving Ribozymes - Progress in Molecular Biology and Translational Science - page 120

CHAPTER FOUR

HDV Family of Self-Cleaving
Ribozymes

Nathan Riccitelli * , Andrej Lupták *

{
* Department of Chemistry, University of California, Irvine, California, USA
† Department of Pharmaceutical Sciences, University of California, Irvine, California, USA
{ Department of Molecular Biology and Biochemistry, University of California, Irvine, California, USA

, † ,

Contents
1. Introduction 124

2. Hepatitis Delta Virus 124

3. HDV Ribozymes 127

3.1 Ribozyme structure 127

3.2 Ribozyme folding 129

4. HDV Ribozymes' Reaction Mechanism 130

4.1 Active-site groups 130

4.2 Metal ion requirements 133

5. Ribozymes Outside of the Hepatitis Delta Virus 135

5.1 The CPEB3 ribozyme 135

5.2 Selection scheme for CPEB3 ribozyme identification 135

5.3 Structural and enzymatic characteristics of the CPEB3 ribozyme 137

5.4 Expression and biological roles of the CPEB3 ribozyme 140

5.5 Bioinformatic identification of ribozymes 141

5.6 Structure-based searches reveal additional HDV ribozymes outside of

mammals 143

5.7 HDV-like ribozymes found using RNABOB 144

5.8 The A. gambiae ribozymes 145

5.9 R2 ribozymes 147

5.10 Additional RT-associated ribozymes 152

5.11 HDV-like ribozyme cores similar to drz-Agam-1 152

5.12 Stronglyocentrotus purpuratus ribozymes 153

5.13 Branchiostoma floridae ribozymes 156

5.14 Petromyzon marinus ribozymes 157

5.15 Nematode ribozymes 157

5.16 HDV-like ribozymes in bacteria and viruses 159

6. Evolutionary Relationship Among HDV-Like Ribozymes 162

References 164