Ribozymes, 2 Volume Set: Principles, Methods, Applications

Ribozymes Provides comprehensive coverage of a core field in the molecular biosciences, bringing together decades of knowledge from the world’s top professionals in the field Timely and unique in its breadth of content, this all-encompassing and authoritative reference on ribozymes documents the great diversity of nucleic acid-based catalysis. It integrates the knowledge gained over the past 35 years in the field and features contributions from virtually every leading expert on the subject. Ribozymes is organized into six major parts. It starts by describing general principles and strategies of nucleic acid catalysis. It then introduces naturally occurring ribozymes and includes the search for new catalytic motifs or novel genomic locations of known motifs. Next, it covers the development and design of engineered ribozymes, before moving on to DNAzymes as a close relative of ribozymes. The next part examines the use of ribozymes for medicinal and environmental diagnostics, as well as for therapeutic tools. It finishes with a look at the tools and methods in ribozyme research, including the techniques and assays for structural and functional characterization of nucleic acid catalysts. The first reference to tie together all aspects of the multi-faceted field of ribozymes Features more than 30 comprehensive chapters in two volumes Covers the chemical principles of RNA catalysis; naturally occurring ribozymes, engineered ribozymes; DNAzymes; ribozymes as tools in diagnostics and therapy, and tools and methods to study ribozymes Includes first-hand accounts of concepts, techniques, and applications by a team of top international experts from leading academic institutions Dedicates half of its content to methods and practical applications, ranging from bioanalytical tools to medical diagnostics to therapeutics Ribozymes is an unmatched resource for all biochemists, biotechnologists, molecular biologists, and bioengineers interested in the topic.

Table of Contents:
Volume 1 Preface xvii Foreword xix Part I Nucleic Acid Catalysis: Principles, Strategies and Biological Function 1 1 The Chemical Principles of RNA Catalysis 3 Timothy J. Wilson and David M. J. Lilley 1.1 RNA Catalysis 3 1.2 Rates of Chemical Reactions and Transition State Theory 4 1.3 Phosphoryl Transfer Reactions in the Ribozymes 5 1.4 Catalysis of Phosphoryl Transfer 6 1.5 General Acid–Base Catalysis in Nucleolytic Ribozymes 8 1.5.1 The Fraction of Active Catalyst, and the pH Dependence of Reaction Rates 9 1.5.2 The Reactivity of General Acids and Bases 13 1.6 pKa Shifting of General Acids and Bases in Nucleolytic Ribozymes 13 1.7 Catalytic Roles of Metal Ions in Ribozymes 14 1.8 The Choice Between General Acid–Base Catalysis and the Use of Metal Ions 17 1.9 The Limitations to RNA Catalysis 18 Acknowledgment 18 References 19 2 Biological Roles of Self-Cleaving Ribozymes 23 Christina E. Weinberg 2.1 Introduction 23 2.2 Use of Self-cleaving Ribozymes for Replication 25 2.2.1 Viroids 25 2.2.2 Viroid-like Satellite RNAs 28 2.2.3 Hepatitis δ Virus RNA 29 2.2.4 Neurospora Varkud Satellite RNAs Replicate Using a DNA Intermediate 29 2.3 Self-cleaving Ribozymes as Part of Transposable Elements 30 2.3.1 R2 Elements: Non-LTR Retrotransposons that Use HDV-like Ribozymes for Retrotransposition 30 2.3.2 HDV-like Ribozymes in Other Non-LTR Retrotransposon Lineages 34 2.3.3 Penelope-like Elements (PLEs) Contain Hammerhead Ribozymes 35 2.3.4 Hammerhead Ribozymes Associated with Repetitive Elements in Schistosoma mansoni 39 2.3.5 Retrozymes: A New Class of Plant Retrotransposons that Contains Hammerhead Ribozymes 40 2.4 Hammerhead Ribozymes with Suggested Roles in mRNA Biogenesis 41 2.5 The glmS Ribozyme Regulates Glucosamine-6-phosphate Levels in Bacteria 41 2.6 The Biological Roles of Many Ribozymes Are Unknown 42 2.7 Conclusion 43 Acknowledgments 43 References 44 Part II Naturally Occurring Ribozymes 55 3 Chemical Mechanisms of the Nucleolytic Ribozymes 57 Timothy J. Wilson and David M. J. Lilley 3.1 The Nucleolytic Ribozymes 57 3.2 Some Nucleolytic Ribozymes AreWidespread 58 3.3 Secondary Structures of Nucleolytic Ribozymes – Junctions and Pseudoknots 58 3.4 Catalytic Players in the Nucleolytic Ribozymes 60 3.5 The Hairpin and VS Ribozymes: The G Plus A Mechanism 61 3.6 The Twister Ribozyme: A G Plus A Variant 66 3.7 The Hammerhead Ribozyme: A 2′-Hydroxyl as a Catalytic Participant 69 3.8 The Hepatitis Delta Virus Ribozyme: A Direct Role for a Metal Ion 72 3.9 The Twister Sister (TS) Ribozyme: Another Metallo-Ribozyme 74 3.10 The Pistol Ribozyme: A Metal Ion as the General Acid 76 3.11 The glmS Ribozyme: Participation of a Coenzyme 78 3.12 A Classification of the Nucleolytic Ribozymes Based on Catalytic Mechanism 79 Acknowledgments 83 References 83 4 TheglmS Ribozyme and Its Multifunctional Coenzyme Glucosamine-6-phosphate 91 Juliane Soukup 4.1 Introduction 91 4.2 Ribozymes 91 4.3 Riboswitches 92 4.4 The glmS Riboswitch/Ribozyme 93 4.5 Biological Function of the glmS Ribozyme 94 4.6 glmS Ribozyme Structure and Function – Initial Biochemical Analyses 95 4.7 glmS Ribozyme Structure and Function – Initial Crystallographic Analysis 98 4.8 Metal Ion Usage by the glmS Ribozyme 99 4.9 In Vitro Selected glmS Catalyst Loses Coenzyme Dependence 101 4.10 Essential Coenzyme GlcN6P Functional Groups 102 4.11 Mechanism of glmS Ribozyme Self-Cleavage 104 4.11.1 Importance of Coenzyme GlcN6P 104 4.11.2 pH-Reactivity Profiles 106 4.11.3 Role of an Active Site Guanine 108 4.12 Potential for Antibiotic Development Affecting glmS Ribozyme/Riboswitch Function 109 Acknowledgments 110 References 110 5 The Lariat Capping Ribozyme 117 Henrik Nielsen, Nicolai Krogh, Benoît Masquida, and Steinar Daae Johansen 5.1 Introduction 117 5.1.1 The Basics 117 5.1.2 A Brief Account of the Discovery of the Lariat Capping Ribozyme 119 5.1.3 Readers Guide to Nomenclature 120 5.1.4 The Species Involved 120 5.2 Reactions Catalyzed by LCrz 121 5.2.1 The Branching Reaction 122 5.2.2 Ligation and Hydrolysis 122 5.2.3 Reaction Conditions 124 5.3 The Structure of the LCrz Core 125 5.3.1 The Detailed Structure of DirLCrz 125 5.3.2 Structure of the Naegleria-type LCrz 126 5.4 Communication Between LCrz and Flanking Elements 128 5.4.1 Group I Ribozyme Switching 128 5.4.2 LC Ribozyme Switching 130 5.4.3 A Role of Spliceosomal Intron I51 in DirLCrz Regulation? 131 5.5 Reflections on the Evolutionary Aspect of LCrz 131 5.5.1 A Model for the Emergence of LCrz 132 5.5.2 An Evolutionary Path to Spliceosomal Splicing? 132 5.6 LCrz as a Research Tool 134 5.7 Conclusions and Unsolved Problems 136 References 138 6 Self-Splicing Group II Introns 143 Isabel Chillón and Marco Marcia 6.1 Introduction 143 6.2 Milestones in the Characterization of Group II Introns 143 6.3 Evolutionary Conservation and Biological Role 145 6.3.1 Phylogenetic Classifications 145 6.3.2 Differentiation and Evolutionarily Acquired Properties 148 6.3.3 Spreading and Survival in the Host Genome 149 6.4 Structural Architecture 152 6.4.1 Secondary Structure and Long-Range Tertiary Interactions 152 6.4.2 Folding 153 6.4.3 Stabilization by Solvent and IEP 154 6.4.4 Active Site and Reaction Mechanism 154 6.5 Lessons and Tools from Group II Intron Research 156 6.5.1 Analogies to Other Splicing Machineries 156 6.5.2 Lessons to Study Other Large Non-coding RNAs 157 6.5.3 Biotechnological Applications of GIIi 157 6.6 Perspectives and Open Questions 158 Acknowledgments 158 References 158 7 The Spliceosome: an RNA–Protein Ribozyme Derived From Ancient Mobile Genetic Elements 169 Erin L. Garside, Oliver A. Kent, and Andrew M. MacMillan 7.1 Discovery of Introns and Splicing 169 7.2 snRNPs and the Spliceosome 170 7.3 The Spliceosomal Cycle 171 7.4 Chemistry of Splicing 173 7.5 Spliceosome Structural Analysis 177 7.6 Spliceosome Structures 177 7.6.1 Pre-spliceosome: Tri-snRNP 177 7.6.2 Pre-spliceosome: A Complex 179 7.6.3 B Complex 179 7.6.4 Activated B Complex 182 7.6.5 C and C* Complexes 183 7.6.6 P Complex 185 7.6.7 Intron Lariat Spliceosome Complex 185 7.7 Insights from Spliceosome Disassembly 187 7.8 Conservation of Spliceosomal and Group II Active Sites 187 7.9 Summary and Perspectives 188 References 189 8 The Ribosome and Protein Synthesis 193 Paul Huter, Michael Graf, and Daniel N. Wilson 8.1 Central Dogma of Molecular Biology 193 8.2 Structure of the E. coli Ribosome 194 8.3 Translation Cycle 194 8.3.1 Initiation 196 8.3.2 Elongation 199 8.3.3 Termination 208 8.3.4 Recycling 211 References 213 9 The RNase P Ribozyme 227 Markus Gößringer, Isabell Schencking, and Roland Karl Hartmann 9.1 Introduction 227 9.2 Bacterial RNase P 229 9.2.1 P RNA Structure and Evolution 229 9.2.2 The Single Protein Subunit 233 9.2.3 P RNAs – Architectural Principles, Variations, Idiosyncrasies 233 9.3 Substrate Interaction 235 9.4 RNA-based Metal Ion Catalysis 247 9.4.1 The Two-metal Ion Mechanism 247 9.4.2 Architecture of the Active Site 250 9.4.3 The “A248/nt −1” Interaction 251 9.4.4 Specific RNase P Cleavage by the P15 Module 253 9.5 RNase P as an Antibiotic Target 254 9.5.1 P RNA as a Target 254 9.5.2 The Bacterial RNase P Holoenzyme as Target 257 9.5.3 P Protein as a Target 258 9.6 Application of RNase P as a Tool in Gene Inactivation 258 9.6.1 The Guide Sequence (GS) Concept 258 9.6.2 EGS Technology in Eukaryotic Cells 259 9.6.3 EGS Oligonucleotides and Recruitment of Human Nuclear-Cytoplasmic RNase P 261 9.6.4 The M1–GS Approach 265 9.6.5 Outlook 266 References 267 10 Ribozyme Discovery in Bacteria 281 Adam Roth and Ronald Breaker 10.1 Introduction 281 10.2 Protein Takeover 282 10.3 Ribozymes as Evolutionary Holdouts 282 10.4 The Role of Serendipity in Early Ribozyme Discoveries 283 10.5 Ribozymes Emerge from Structured Noncoding RNA Searches 285 10.6 Ribozymes Beget Ribozymes 289 10.7 Ribozyme Dispersal Driven by Association with Selfish Elements 291 10.8 Domesticated Ribozymes 292 10.9 New Ribozymes from Old 294 10.10 Will New ncRNAs Broaden the Scope of RNA Catalysis? 295 Acknowledgments 296 References 296 11 Small Self-Cleaving Ribozymes in the Genomes of Vertebrates 303 Marcos de la Peña 11.1 The Family of Small Self-Cleaving Ribozymes in Eukaryotic Genomes: From Retrotransposition to Domestication 303 11.2 The Widespread Case of the Hammerhead Ribozyme: From Bacteria to Vertebrate Genomes 304 11.2.1 The Discontinuous HHR in Mammals 307 11.2.2 Intronic HHRs in Amniotes 310 11.3 Other Intronic HHRs in Amniotes: Small Catalytic RNAs in Search of a Function 315 11.4 The Family of the Hepatitis D Virus Ribozymes 318 11.4.1 An Intronic HDV-Like Ribozyme Conserved in the Genome of Mammals 320 11.5 Other Small Self-Cleaving Ribozymes Hidden in the Genomes of Vertebrates? 322 References 323 Part III Engineered Ribozymes 329 12 Phosphoryl Transfer Ribozymes 331 Razvan Cojocaru and Peter J. Unrau 12.1 Introduction 331 12.2 Kinase Ribozymes 332 12.3 Glycosidic Bond Forming Ribozymes 336 12.4 Capping Ribozymes 340 12.5 Ligase Ribozymes 344 12.6 Polymerase Ribozymes 351 12.7 Summary 353 References 353 13 RNA Replication and the RNA Polymerase Ribozyme 359 Falk Wachowius and Philipp Holliger 13.1 Introduction 359 13.2 Nonenzymatic RNA Polymerization 360 13.3 Enzymatic RNA Polymerization 361 13.4 Essential Requirements for an RNA Replicator 363 13.4.1 Likelihood of Replicating Sequences in RNA Sequence Space 364 13.4.2 Reaction Conditions for RNA Replication 366 13.4.3 The Strand Separation Problem 367 13.5 The Class I Ligase and the First RNA Polymerase Ribozymes 367 13.6 Structural Insight into the Catalytic Core of the RNA Polymerase Ribozyme 372 13.7 Selection for Improved Polymerase Activity I 374 13.8 Selection for Improved Polymerase Activity II 377 13.9 Conclusion and Outlook 380 References 381 14 Maintenance of Genetic Information in the First Ribocell 387 Ádám Kun 14.1 The Ribocell and the Stages of the RNAWorld 387 14.1.1 Replication of the Genetic Information 389 14.1.2 On the Metabolic Complexity of Ribocells 389 14.2 The Error Thresholds 391 14.2.1 Introducing the Error Threshold 391 14.2.2 The Fitness Landscape and Neutrality of Mutations 393 14.3 Compartmentalization 396 14.3.1 Surface Metabolism and Transient Compartmentalization 397 14.3.2 The Stochastic Corrector Model 399 14.4 Minimal Gene Content of the First Ribocell 401 14.4.1 Intermediate Metabolism 402 14.4.2 Cell-Level Processes 404 Acknowledgments 406 References 406 15 Ribozyme-Catalyzed RNA Recombination 419 Benedict A. Smail and Niles Lehman 15.1 Introduction 419 15.2 RNA Recombination Chemistry 420 15.3 Azoarcus Group I Intron 421 15.4 Crystal Structure 422 15.5 Mechanism 422 15.6 Model for Prebiotic Chemistry 423 15.7 Spontaneous Self-assembly of Azoarcus RNA Fragments 425 15.8 Autocatalysis 428 15.9 Cooperative Self-assembly 429 15.10 Game Theoretic Treatment 430 15.11 Significance of Game Theoretic Treatments 432 15.12 Other Recombinase Ribozymes 433 15.13 Conclusions 435 References 436 16 Engineering of Hairpin Ribozymes for RNA Processing Reactions 439 Robert Hieronymus, Jikang Zhu, Bettina Appel, and Sabine Müller 16.1 Introduction 439 16.2 The Naturally Occurring Hairpin Ribozyme 440 16.3 Structural Variants of the Hairpin Ribozyme 442 16.4 Hairpin Ribozymes that are Regulated by External Effectors 443 16.5 Twin Ribozymes for RNA Repair and Recombination 446 16.6 Hairpin Ribozymes as RNA Recombinases 449 16.7 Self-Splicing Hairpin Ribozymes 452 16.8 Closing Remarks 454 References 456 17 Engineering of the Neurospora Varkud Satellite Ribozyme for Cleavage of Nonnatural Stem-Loop Substrates 463 Pierre Dagenais, Julie Lacroix-Labonté, Nicolas Girard, and Pascale Legault 17.1 Introduction 463 17.2 Simple Primary and Secondary Structure Changes Compatible with Substrate Cleavage by the VS Ribozyme 464 17.2.1 Circular Permutations and trans Cleavage 464 17.2.2 The I/V Kissing-Loop Interaction and the Associated Conformational Change in SLI 466 17.2.3 Summary of SLI Sequences Compatible with Cleavage by the Wild-Type VS Ribozyme 468 17.3 The Structural Context 470 17.3.1 NMR Investigations of the VS Ribozyme 470 17.3.2 Crystal Structures of a Dimeric Form of the VS Ribozyme 473 17.3.3 Open and Closed States of the S/R Complex 473 17.4 Structure-Guided Engineering Studies 474 17.4.1 Helix-Length Compensation 474 17.4.2 Kissing-Loop Substitutions 475 17.4.3 Role of KLI Dynamics in the Cleavage Reaction 476 17.4.4 Improving the Cleavage Activity of a Designer Ribozyme 478 17.5 Summary and Future Prospects for VS Ribozyme Engineering 480 References 481 18 Chemical Modifications in Natural and Engineered Ribozymes 487 Stephanie Kath-Schorr 18.1 Introduction 487 18.2 Chemical Modifications to Study Natural Ribozymes 488 18.2.1 Modified Nucleotides for Mechanistic and Structural Studies on Ribozymes 488 18.2.2 Stabilization of Ribozymes by Chemical Modifications for in Cell Applications 489 18.3 In Vitro Selection with Chemically Modified Nucleotides: Expanding the Scope of DNA and RNA Catalysis 490 18.3.1 General Aspects for In Vitro Selection Using Unnatural Nucleotides 491 18.3.2 Selection of Deoxyribozymes with Modified Nucleotides 492 18.3.3 Artificial Ribozymes with Nonnatural Nucleobases 494 18.3.4 Catalysts With Nonnatural Backbones: XNAzymes 495 18.4 Outlook 495 References 496 19 Ribozymes for Regulation of Gene Expression 505 Julia Stifel and Jörg S. Hartig 19.1 Introduction 505 19.2 Conditional Gene Expression Control by Riboswitches 505 19.3 Allosteric Ribozymes as Engineered Riboswitches 506 19.4 In Vitro Selection Methods 507 19.5 In Vivo Screening Methods 508 19.6 Rational Design of Allosteric Ribozymes 511 19.7 Applications of Aptazymes for Gene Regulation 512 References 514 20 Development of Flexizyme Aminoacylation Ribozymes and Their Applications 519 Takayuki Katoh, Yuki Goto, Toby Passioura, and Hiroaki Suga 20.1 Introduction 519 20.2 The First Ribozymes Catalyzing Acyl Transfer to RNAs 520 20.3 The ATRib Variant Family: Ribozymes Catalyzing tRNA Aminoacylation via Self-Acylated Intermediates 521 20.4 Prototype Flexizymes: Ribozymes Catalyzing Direct tRNA Aminoacylation 523 20.5 Flexizymes: Versatile Ribozymes for the Preparation of Aminoacyl-tRNAs 526 20.6 Application of Flexizymes to Genetic Code Reprogramming 527 20.7 Development of Orthogonal tRNA/Ribosome Pairs Using Mutant Flexizymes 530 20.8 In Vitro Selection of Bioactive Peptides Containing nPAAs Through RaPID Display 532 20.9 tRid: A Method for Selective Removal of tRNAs from an RNA Pool 535 20.10 Use of a Natural Small RNA Library Lacking tRNA for In Vitro Selection of a Folic Acid Aptamer: Small RNA Transcriptomic SELEX 535 20.11 Summary and Perspective 537 Acknowledgments 539 References 539 21 In Vitro Selected (Deoxy)ribozymes that Catalyze Carbon–Carbon Bond Formation 545 Michael Famulok 21.1 Introduction 545 21.2 Diels–Alderase Ribozymes 546 21.3 Aldolase Ribozyme 547 21.4 A DNAzyme that Catalyzes a Friedel–Crafts Reaction 548 21.5 Alkylating Ribozymes 550 21.6 Conclusion 554 References 555 22 Nucleic Acid-Catalyzed RNA Ligation and Labeling 557 Mohammad Ghaem Maghami and Claudia Höbartner 22.1 Introduction 557 22.2 Ribozymes for RNA Labeling at Internal Positions 558 22.2.1 Fluorescein Iodoacetamide Reactive Ribozyme 558 22.2.2 Genomically Derived Epoxide Reactive Ribozyme 559 22.2.3 Twin Ribozyme 561 22.2.4 DNA as a Catalyst for Ligation of Modified RNA 562 22.2.5 Site-Specific Internal Labeling of RNA with DNA Enzymes 563 22.3 RNA-Catalyzed Labeling of RNA at the 3′-end 564 22.4 Potential Ribozymes for RNA Labeling at the 5′-end 565 22.5 Conclusions 566 Acknowledgments 566 References 568 Volume 2 Preface xiii Foreword xv Part IV DNAzymes 571 23 The Chemical Repertoire of DNA Enzymes 573 Marcel Hollenstein 24 Light-Utilizing DNAzymes 621 Adam Barlev and Dipankar Sen 25 Diverse Applications of DNAzymes in Computing and Nanotechnology 633 Matthew R. Lakin, Darko Stefanovic, and Milan N. Stojanovic Part V Ribozymes/DNAzymes in Diagnostics and Therapy 661 26 Optimization of Antiviral Ribozymes 663 Alfredo Berzal-Herranz and Cristina Romero-López 27 DNAzymes as Biosensors 685 Lingzi Ma and Juewen Liu 28 Compartmentalization-Based Technologies for In Vitro Selection and Evolution of Ribozymes and Light-Up RNA Aptamers 721 Farah Bouhedda and Michael Ryckelynck Part VI Tools and Methods to Study Ribozymes 739 29 Elucidation of Ribozyme Mechanisms at the Example of the Pistol Ribozyme 741 Christoph Falschlunger, Josef Leiter, and Ronald Micura 30 Strategies for Crystallization of Natural Ribozymes 753 Benoît Masquida, Diana Sibrikova, and Maria Costa 31 NMR Spectroscopic Investigation of Ribozymes 785 Bozana Knezic, Oliver Binas, Albrecht Eduard Völklein, and Harald Schwalbe 32 Studying Ribozymes with Electron Paramagnetic Resonance Spectroscopy 817 Olav Schiemann 33 Computational Modeling Methods for 3D Structure Prediction of Ribozymes 861 Pritha Ghosh, Chandran Nithin, Astha Joshi, Filip Stefaniak, Tomasz K. Wirecki, and Janusz M. Bujnicki Index 883

About the Author :
Sabine Müller is Full Professor for Biochemistry/Bioorganic Chemistry at University Greifswald (Germany), and is a member of the Leibniz-Sozietät der Wissenschaften zu Berlin and of AcademiaNet. She has been working in the field of RNA engineering and has made important contributions to ribozyme research. Benoît Masquida is a Research Director at Centre National de la Recherche Scientifique, and carries on research and teaching activities at the University of Strasbourg (France). He made important contributions in the field of RNA structural biology, notably through identification of new RNA folds and their evolutionary relationships. Wade Winkler is Professor of Cell Biology and Molecular Genetics at the University of Maryland (USA), and has authored multiple influential publications on the different types of regulatory RNAs in bacteria.