Ribozymes . Volume 1 : principles, methods, applications / / edited by Sabine Müller, Benoît Masquida, Wade Winkler

• Record Nr.: UNINA9910555257903321
• Pubbl/distr/stampa: Weinheim, Germany : , : Wiley-VCH, , [2021]; ©2021
• ISBN: 3-527-81455-8; 3-527-81452-3; 3-527-81453-1
• Descrizione fisica: 1 online resource (1076 pages)
• Disciplina: 572.88
• Soggetti: Genetic regulation; Catalytic RNA; Electronic books.
• Lingua di pubblicazione: Inglese
• Formato: Materiale a stampa
• Livello bibliografico: Monografia
• Nota di bibliografia: Includes bibliographical references and index.
• Nota di contenuto: Intro -- Table of Contents -- Title Page -- Title Page -- Copyright -- Preface -- Foreword -- References -- Volume 1 -- Part I: Nucleic Acid Catalysis: Principles, Strategies and Biological Function -- 1 The Chemical Principles of RNA Catalysis -- 1.1 RNA Catalysis -- 1.2 Rates of Chemical Reactions and Transition State Theory -- 1.3 Phosphoryl Transfer Reactions in the Ribozymes -- 1.4 Catalysis of Phosphoryl Transfer -- 1.5 General Acid-Base Catalysis in Nucleolytic Ribozymes -- 1.6 pKa Shifting of General Acids and Bases in Nucleolytic Ribozymes -- 1.7 Catalytic Roles of Metal Ions in Ribozymes -- 1.8 The Choice Between General Acid-Base Catalysis and the Use of Metal Ions -- 1.9 The Limitations to RNA Catalysis -- Acknowledgment -- References -- 2 Biological Roles of Self‐Cleaving Ribozymes -- 2.1 Introduction -- 2.2 Use of Self‐cleaving Ribozymes for Replication -- 2.3 Self‐cleaving Ribozymes as Part of Transposable Elements -- 2.4 Hammerhead Ribozymes with Suggested Roles in mRNA Biogenesis -- 2.5 The glmS Ribozyme Regulates Glucosamine‐6‐phosphate Levels in Bacteria -- 2.6 The Biological Roles of Many Ribozymes Are Unknown -- 2.7 Conclusion -- Acknowledgments -- References -- Part II: ; Naturally Occurring Ribozymes -- 3 Chemical Mechanisms of the Nucleolytic Ribozymes -- 3.1 The Nucleolytic Ribozymes -- 3.2 Some Nucleolytic Ribozymes Are Widespread -- 3.3 Secondary Structures of Nucleolytic Ribozymes - Junctions and Pseudoknots -- 3.4 Catalytic Players in the Nucleolytic Ribozymes -- 3.5 The Hairpin and VS Ribozymes: The G Plus A Mechanism -- 3.6 The Twister Ribozyme: A G Plus A Variant -- 3.7 The Hammerhead Ribozyme: A 2'‐Hydroxyl as a Catalytic Participant -- 3.8 The Hepatitis Delta Virus Ribozyme: A Direct Role for a Metal Ion -- 3.9 The Twister Sister (TS) Ribozyme: Another Metallo‐Ribozyme.; 3.10 The Pistol Ribozyme: A Metal Ion as the General Acid -- 3.11 The glmS Ribozyme: Participation of a Coenzyme -- 3.12 A Classification of the Nucleolytic Ribozymes Based on Catalytic Mechanism -- Acknowledgments -- References -- Note -- 4 The glmS Ribozyme and Its Multifunctional Coenzyme Glucosamine‐6‐phosphate -- 4.1 Introduction -- 4.2 Ribozymes -- 4.3 Riboswitches -- 4.4 The glmS Riboswitch/Ribozyme -- 4.5 Biological Function of the glmS Ribozyme -- 4.6 glmS Ribozyme Structure and Function - Initial Biochemical Analyses -- 4.7 glmS Ribozyme Structure and Function - Initial Crystallographic Analysis -- 4.8 Metal Ion Usage by the glmS Ribozyme -- 4.9 In Vitro Selected glmS Catalyst Loses Coenzyme Dependence -- 4.10 Essential Coenzyme GlcN6P Functional Groups -- 4.11 Mechanism of glmS Ribozyme Self‐Cleavage -- 4.12 Potential for Antibiotic Development Affecting glmS Ribozyme/Riboswitch Function -- Acknowledgments -- References -- 5 The Lariat Capping Ribozyme -- 5.1 Introduction -- 5.2 Reactions Catalyzed by LCrz -- 5.3 The Structure of the LCrz Core -- 5.4 Communication Between LCrz and Flanking Elements -- 5.5 Reflections on the Evolutionary Aspect of LCrz -- 5.6 LCrz as a Research Tool -- 5.7 Conclusions and Unsolved Problems -- References -- 6 Self‐Splicing Group II Introns -- 6.1 Introduction -- 6.2 Milestones in the Characterization of Group II Introns -- 6.3 Evolutionary Conservation and Biological Role -- 6.4 Structural Architecture -- 6.5 Lessons and Tools from Group II Intron Research -- 6.6 Perspectives and Open Questions -- Acknowledgments -- References -- 7 The Spliceosome: an RNA-Protein Ribozyme Derived From Ancient Mobile Genetic Elements -- 7.1 Discovery of Introns and Splicing -- 7.2 snRNPs and the Spliceosome -- 7.3 The Spliceosomal Cycle -- 7.4 Chemistry of Splicing -- 7.5 Spliceosome Structural Analysis.; 7.6 Spliceosome Structures -- 7.7 Insights from Spliceosome Disassembly -- 7.8 Conservation of Spliceosomal and Group II Active Sites -- 7.9 Summary and Perspectives -- References -- 8 The Ribosome and Protein Synthesis -- 8.1 Central Dogma of Molecular Biology -- 8.2 Structure of the E. coli Ribosome -- 8.3 Translation Cycle -- References -- 9 The RNase P Ribozyme -- 9.1 Introduction -- 9.2 Bacterial RNase P -- 9.3 Substrate Interaction -- 9.4 RNA‐based Metal Ion Catalysis -- 9.5 RNase P as an Antibiotic Target -- 9.6 Application of RNase P as a Tool in Gene Inactivation -- References -- 10 Ribozyme Discovery in Bacteria -- 10.1 Introduction -- 10.2 Protein Takeover -- 10.3 Ribozymes as Evolutionary Holdouts -- 10.4 The Role of Serendipity in Early Ribozyme Discoveries -- 10.5 Ribozymes Emerge from Structured Noncoding RNA Searches -- 10.6 Ribozymes Beget Ribozymes -- 10.7 Ribozyme Dispersal Driven by Association with Selfish Elements -- 10.8 Domesticated Ribozymes -- 10.9 New Ribozymes from Old -- 10.10 Will New ncRNAs Broaden the Scope of RNA Catalysis? -- Acknowledgments -- References -- 11 Small Self‐Cleaving Ribozymes in the Genomes of Vertebrates -- 11.1 The Family of Small Self‐Cleaving Ribozymes in Eukaryotic Genomes: From ; Retrotransposition to Domestication -- 11.2 The Widespread Case of the Hammerhead Ribozyme: From Bacteria to Vertebrate Genomes -- 11.3 Other Intronic HHRs in Amniotes: Small Catalytic RNAs in Search of a Function -- 11.4 The Family of the Hepatitis D Virus Ribozymes -- 11.5 Other Small Self‐Cleaving Ribozymes Hidden in the Genomes of Vertebrates? -- References -- Part III: Engineered Ribozymes -- 12 Phosphoryl Transfer Ribozymes -- 12.1 Introduction -- 12.2 Kinase Ribozymes -- 12.3 Glycosidic Bond Forming Ribozymes -- 12.4 Capping Ribozymes -- 12.5 Ligase Ribozymes -- 12.6 Polymerase Ribozymes -- 12.7 Summary.; References -- 13 RNA Replication and the RNA Polymerase Ribozyme -- 13.1 Introduction -- 13.2 Nonenzymatic RNA Polymerization -- 13.3 Enzymatic RNA Polymerization -- 13.4 Essential Requirements for an RNA Replicator -- 13.5 The Class I Ligase and the First RNA Polymerase Ribozymes -- 13.6 Structural Insight into the Catalytic Core of the RNA Polymerase Ribozyme -- 13.7 Selection for Improved Polymerase Activity I -- 13.8 Selection for Improved Polymerase Activity II -- 13.9 Conclusion and Outlook -- References -- 14 Maintenance of Genetic Information in the First Ribocell -- 14.1 The Ribocell and the Stages of the RNA World -- 14.2 The Error Thresholds -- 14.3 Compartmentalization -- 14.4 Minimal Gene Content of the First Ribocell -- Acknowledgments -- References -- 15 Ribozyme‐Catalyzed RNA Recombination -- 15.1 Introduction -- 15.2 RNA Recombination Chemistry -- 15.3 Azoarcus Group I Intron -- 15.4 Crystal Structure -- 15.5 Mechanism -- 15.6 Model for Prebiotic Chemistry -- 15.7 Spontaneous Self‐assembly of Azoarcus RNA Fragments -- 15.8 Autocatalysis -- 15.9 Cooperative Self‐assembly -- 15.10 Game Theoretic Treatment -- 15.11 Significance of Game Theoretic Treatments -- 15.12 Other Recombinase Ribozymes -- 15.13 Conclusions -- References -- 16 Engineering of Hairpin Ribozymes for RNA Processing Reactions -- 16.1 Introduction -- 16.2 The Naturally Occurring Hairpin Ribozyme -- 16.3 Structural Variants of the Hairpin Ribozyme -- 16.4 Hairpin Ribozymes that are Regulated by External Effectors -- 16.5 Twin Ribozymes for RNA Repair and Recombination -- 16.6 Hairpin Ribozymes as RNA Recombinases -- 16.7 Self‐Splicing Hairpin Ribozymes -- 16.8 Closing Remarks -- References -- 17 Engineering of the Neurospora Varkud Satellite Ribozyme for Cleavage of Nonnatural Stem‐Loop Substrates -- 17.1 Introduction.; 17.2 Simple Primary and Secondary Structure Changes Compatible with Substrate Cleavage by the VS Ribozyme -- 17.3 The Structural Context -- 17.4 Structure‐Guided Engineering Studies -- 17.5 Summary and Future Prospects for VS Ribozyme Engineering -- References -- 18 Chemical Modifications in Natural and Engineered Ribozymes -- 18.1 Introduction -- 18.2 Chemical Modifications to Study Natural Ribozymes -- 18.3 In Vitro Selection with Chemically Modified Nucleotides: Expanding the Scope of DNA and RNA Catalysis -- 18.4 Outlook -- References -- 19 Ribozymes for Regulation of Gene Expression -- 19.1 Introduction -- 19.2 Conditional Gene Expression Control by Riboswitches -- 19.3 Allosteric Ribozymes as Engineered Riboswitches -- 19.4 In Vitro Selection Methods -- 19.5 In Vivo Screening Methods -- 19.6 Rational Design of Allosteric Ribozymes -- 19.7 Applications of Aptazymes for Gene Regulation -- References -- 20 Development of Flexizyme Aminoacylation Ribozymes and Their Applications -- 20.1 Introduction -- 20.2 The First Ribozymes Catalyzing Acyl Transfer to RNAs -- 20.3 The ATRib Variant Family: Ribozymes Catalyzing tRNA Aminoacylation via Self‐Acylated Intermediates -- 20.4 Prototype Flexizymes: Ribozymes Catalyzing Direct tRNA Aminoacylation -- 20.5 Flexizymes: Versatile Ribozymes ; for the Preparation of Aminoacyl‐tRNAs -- 20.6 Application of Flexizymes to Genetic Code Reprogramming -- 20.7 Development of Orthogonal tRNA/Ribosome Pairs Using Mutant Flexizymes -- 20.8 In Vitro Selection of Bioactive Peptides Containing nPAAs Through RaPID Display -- 20.9 tRid: A Method for Selective Removal of tRNAs from an RNA Pool -- 20.10 Use of a Natural Small RNA Library Lacking tRNA for In Vitro Selection of a Folic Acid Aptamer: Small RNA Transcriptomic SELEX -- 20.11 Summary and Perspective -- Acknowledgments -- References.; 21 In Vitro Selected (Deoxy)ribozymes that Catalyze Carbon-Carbon Bond Formation.