Recoding: Expansion of Decoding Rules Enriches Gene Expression (eBook)

Foreword 5
Preface 7
Contents 15
Contributors 17
Part I Redefinition 20
1 Selenocysteine Biosynthesis, Selenoproteins, and Selenoproteomes 21
1.1 UGA is Recoded for Sec 22
1.1.1 Variations in the Genetic Code 22
1.2 Biosynthesis of Sec 23
1.2.1 Unique Features of Sec tRNA 24
1.2.2 tRNA Knockout and Transgenic Mouse Models 25
1.2.3 Aminoacylation of Sec tRNA [Ser]Sec 25
1.2.4 Phosphoseryl-tRNA [Ser]Sec kinase 26
1.2.5 Sec Synthase (SecS) and Selenophosphate Synthetase (SPS) 26
1.2.6 The Sec biosynthetic pathway 28
1.3 Identification of Selenoproteins in Sequence Databases 29
1.4 Selenoproteins 30
1.4.1 Overview of Selenoprotein Functions 31
1.5 Selenoproteomes 32
1.6 Thioredoxin Reductase and Cancer 33
1.7 Selenoprotein Knockout Mouse Models 34
1.8 Sec tRNA Knockout and Transgenic Mouse Models 34
References 40
2 Reprogramming the Ribosome for Selenoprotein Expression: RNA Elements and Protein Factors 46
2.1 Selenium, Selenocysteine, and Selenoproteins 46
2.2 The Mechanism of Selenocysteine Incorporation in Eukaryotes 47
2.2.1 Identification of Cis-Acting Factors in Eukaryotes 47
2.2.2 Identification of Trans-Acting Factors in Eukaryotes 52
2.3 Efficiency of Selenocysteine Incorporation in Eukaryotes 55
2.4 Hierarchy of Selenoprotein Synthesis 58
2.5 Other Factors Effecting Differential Selenoprotein Expression 60
2.6 Where do Selenoprotein mRNA Decoding Complexes Assemble? 61
2.7 Elucidating the Functions of Selenoproteins 62
2.8 Summary 62
References 64
3 Translation of UAG as Pyrrolysine 70
3.1 Introduction 71
3.2 The Discovery and Biological Context of Pyrrolysine 71
3.3 Novel Functionality Underlies Pyrrolysine Addition to the Genetic Code 74
3.4 The pyl Gene Cluster 74
3.5 Structure and Binding of tRNA Pyl by PylS 77
3.6 Pyrrolysine Recognition by PylS and PylSc 79
3.7 PylS and tRNA Pyl -Based Amber Suppression in E. coli as a Tool for Biotechnology 80
3.8 Transmissible Biosynthesis and Genetic Encoding of Pyrrolysine 81
3.9 Predictions of UAG as Sense and Stop Codon in pyl -Containing Organisms 82
3.10 UAG Is Both Stop and Sense in M. acetivorans 84
3.11 Amber Suppression May Not Be Enough for Methanogenic Archaea 87
3.12 A Putative Pyrrolysine Insertion Sequence 88
3.13 Multiple Termination and Elongation Factors in Methanosarcina spp 90
3.14 Beyond Pyrrolysine 91
References 92
4 Specification of Standard Amino Acids by Stop Codons 95
4.1 Introduction 95
4.2 Translation Termination and Programmed Stop Codon Readthrough 96
4.3 Readthrough in Viruses and Phages 99
4.4 Biological Relevance of Stop Codon Readthrough in Cells 102
4.5 Identification of Readthrough Sites in Genomes 105
4.6 Programmed Readthrough as a Tool to Study Translation Termination 106
4.7 Whats Next? Remaining Questions and Objectives 109
References 111
5 Ribosome Skipping: Stop-Carry On or StopGo Translation 117
5.1 Picornavirus 2A Sequences 118
5.2 Analyses Using Artificial Polyprotein Systems 119
5.3 The Co-translational Model of 2A-Mediated Cleavage 122
5.3.1 Roles for Conserved and Non-Conserved Portions of 2A 122
5.3.2 Why Is the Glycine-Proline Peptide Bond Not Formed? 124
5.4 Testing the Co-translational Model 125
5.4.1 Ribosomal Pausing at 2A 125
5.4.2 The 2A Reaction Takes Place at the Ribosomal Decoding Centre 125
5.4.3 Translation Terminating Release Factors and the 2A Reaction 127
5.5 Refining the Co-translational Model 129
5.5.1 Binding/Dissociation of Prolyl-tRNA 129
5.5.2 eRF Activity 129
5.5.3 ''Regulation'' of the 2A Reaction? 130
5.6 2A-Like Sequences 131
5.7 Concluding Remarks 133
References 134
6 Recoding Therapies for Genetic Diseases 138
6.1 Recoding Premature Stop Codons Using Small Molecules 138
6.1.1 Aminoglycosides and Their Derivatives 140
6.1.2 Non-aminoglycoside Compounds 150
6.1.3 Outstanding Questions Regarding Recoding Premature Termination Codons 152
6.2 Recoding Premature Stop Codons Using Suppressor tRNAs 154
6.3 Recoding Mutations using Antisense Oligonucleotides 154
6.4 Concluding Remarks 156
References 157
Part II Frameshifting Redirection of Linear Readout 162
7 Pseudoknot-Dependent Programmed 1 Ribosomal Frameshifting: Structures, Mechanisms and Models 163
7.1 Introduction 164
7.2 The Nature, Occurrence and Role of Ribosomal Frameshifting 166
7.3 The Structure of Ribosomal Frameshifting Signals 167
7.4 Stimulatory RNA Structures 167
7.4.1 The IBV Pseudoknot and Relatives 168
7.4.2 The RSV Pseudoknot and Interstem Elements 172
7.4.3 The ''Kinked'' Pseudoknots 173
7.4.4 The Luteoviral Pseudoknots and Loop--Helix Interactions 174
7.4.5 Long-Range Pseudoknots 174
7.5 Mechanistic Aspects of Ribosomal Frameshifting 174
7.5.1 tRNA Slippage 175
7.5.2 Ribosomal Pausing 175
7.5.3 The Stimulatory RNA Resists Unwinding by the Ribosome 176
7.5.4 A Role for trans-Acting Protein Factors? 178
7.5.5 Conceivable Points for Frameshifting During the Elongation Cycle 178
7.6 Models of Frameshifting 179
7.6.1 The Integrated and 9Å Models 179
7.6.2 The Simultaneous Slippage Model 181
7.6.3 The Dynamic Model 181
7.6.4 The Mechanical Model 182
7.6.5 The Three-tRNA Model 184
7.7 Perspective 185
References 186
8 Programmed 1 Ribosomal Frameshift in the Human Immunodeficiency Virus of Type 1 189
8.1 Characteristics of the Slippery Sequence and the Frameshift Stimulatory Signal of HIV-1 189
8.2 Models of 1 Ribosomal Frameshift in HIV-1 192
8.3 Rates of Initiation and Elongation of Translation and Their Effect on the Frameshift 198
8.4 Remaining Questions to Address 199
8.5 The Frameshift Event as a Target for Novel Anti-HIV Drugs 201
8.6 Conclusions and Perspectives 202
References 203
9 Ribosomal Frameshifting in Decoding Plant Viral RNAs 207
9.1 Introduction 208
9.1.1 Frameshifting Plant Viruses 208
9.1.2 Why Frameshift? 208
9.1.3 Proposed Mechanisms of -1 Frameshift Stimulation 211
9.2 Plant Virus Frameshift Elements 213
9.2.1 Luteoviridae 213
9.2.2 Frameshift Stimulators Involving Long-Distance Base Pairing 214
9.2.3 Polerovirus and Enamovirus 217
9.2.4 Frameshift Stimulators with Compact Pseudoknots 217
9.2.5 Sobemoviruses 223
9.2.6 Closteroviruses 225
9.2.7 Carlaviruses 226
9.2.8 Potyviruses 227
9.3 Summary 228
References 229
10 Programmed Frameshifting in Budding Yeast 235
10.1 Introduction 236
10.2 Programmed +1 Frameshifting in S. cerevisiae 236
10.2.1 Ty Transposons in S. cerevisiae 237
10.2.1.1 Evidence for +1 Frameshifting in Ty1 Elements 237
10.2.1.2 The Purpose of +1 Frameshifting for Ty1 Propagation 239
10.2.1.3 Ty1-Type Programmed Frameshifting Occurs in Multiple-Related Ty-Family Elements 241
10.2.1.4 Evidence for +1 Frameshifting in Ty3 Elements 241
10.2.1.5 Translational Frameshifting Induced by Near-Cognate Peptidyl-tRNAs 242
10.2.2 EST3 Gene in S. cerevisiae 243
10.2.2.1 Identification of the Downstream Stimulator Sequence 244
10.2.3 ABP140 Gene in S. cerevisiae 245
10.2.4 OAZ1 Gene in S. cerevisiae 245
10.2.5 Bioinformatic Analysis Identifies Novel +1 Frameshift Sites in S. cerevisiae 246
10.2.6 Factors That Stimulate Programmed +1 Frameshifting in S. cerevisiae 247
10.2.6.1 Near-Cognate Peptidyl-tRNAs Stimulate +1 Frameshifting 247
10.2.6.2 Frameshifting Stimulated by tRNA Competition 247
10.2.6.3 Cis-Acting RNA Sequences That Stimulate +1 Programmed Frameshifting 248
10.3 Evolution of +1 Programmed Frameshift Systems in Budding Yeasts 249
10.3.1 Phylogeny of Retrotransposons in Budding Yeast 249
10.3.2 Phylogeny of Frameshifting in the Three Chromosomal Genes 250
10.3.3 Phylogeny of tRNAs Important to Programmed +1 Frameshifting 250
10.3.4 What Persistence Over Evolutionary Time Implies About the Function of Programmed Frameshift 250
10.4 Programmed 1 Frameshifting in S. cerevisiae 251
10.5 The L-A virus 252
10.5.1 Role of the Frameshift in Virus Function 253
10.5.2 Evidence for other -1 Programmed Frameshift Sites in S. cerevisiae 255
10.6 General Lessons from Analysis of Programmed Frameshifting in Budding Yeast 256
10.6.1 How Do +1 Frameshift Signals Manipulate the Translation Machinery? 256
10.6.2 -1 Frameshift Signals May Also Favor a Kinetically Unfavorable Event 258
References 259
11 Recoding in Bacteriophages 262
11.1 Tailed dsDNA Phages: Frameshift in the Tail Genes 263
11.2 Tailed dsDNA Phages: C-Terminal Domains 265
11.3 ssRNA Phages 268
11.4 Undiscovered Examples of Phage Recoding? 269
References 270
12 Programmed Ribosomal --1 Frameshifting as a Tradition: The Bacterial Transposable Elements of the IS3 Family 272
12.1 Comparative Analysis of IS 3 Family Members (ISFinder Database, June 2008) 275
12.1.1 The Frameshift Motifs 277
12.1.2 Upstream Stimulators, Shine--Dalgarno-Like Sequences 280
12.1.3 Downstream Stimulatory Structures 283
12.1.3.1 Role in Frameshifting 283
12.1.3.2 Stem Loops 284
12.1.3.3 H-Type Pseudoknots 285
12.1.3.4 ALIL-PK 287
12.1.4 The No-Stimulator Cases 287
12.2 Functional Analysis of Typical Cases 288
12.2.1 IS 911 288
12.2.2 IS 3 289
12.2.3 IS 3411 290
12.3 Lessons from IS 3 Family Studies 290
12.3.1 A Summary of How Motifs and Stimulators Combine in the IS 3 Family 290
12.3.2 The Three Ways of Translational -1 Frameshifting in Bacteria 290
12.4 Concluding Remarks 291
References 292
13 Autoregulatory Frameshifting in Antizyme Gene Expression Governs Polyamine Levels from Yeast to Mammals 294
13.1 Alternative Start Codons and Possible Regulation Through the 3 UTR 297
13.2 The Antizyme Gene Family 298
13.3 Shift Sites 299
13.4 5 Stimulators of Frameshifting 302
13.5 3 Stimulators of Frameshifting 305
13.6 Mechanism of Frameshifting 309
References 311
14 Sequences Promoting Recoding Are Singular Genomic Elements 314
14.1 Singular Genomic Elements 314
14.2 Sequences Promoting Ribosomal Frameshifting as Singular Genomic Elements 315
14.2.1 +1 Frameshifting Cassette in Bacterial Release Factor 2 mRNA 316
14.2.2 -1 Frameshifting Cassette in Coronavirus Polyprotein-Encoding Gene 321
14.3 Cars and Ribosomes, Fast and Furious: Role of mRNA in the Accuracy of Translation 321
14.4 Strategies for Searching Recoding Cases as Singular Elements 324
14.5 Possible Functions of Products Generated by Low-Level Aberrant Translation 328
14.6 Conclusions 329
References 330
15 Mutants That Affect Recoding 334
15.1 Introduction 335
15.2 Bacterial Mutants Affecting the Fidelity of Decoding 335
15.2.1 The Ribosome as a ''Recognition Screen'' for tRNAs 336
15.2.1.1 The First Ribosomal Accuracy Mutants 336
15.2.2 The Decoding Mechanism, Streptomycin and Ribosomal Proteins S4, S5, and S12 Insights from Crystallography
15.2.2.1 Decoding Center rRNA Mutants 338
15.2.2.2 The Intersubunit Bridges 338
15.2.2.3 The Peptidyltransferase Center and Beyond 340
15.2.3 Factor Interaction Sites 341
15.2.3.1 The GTPase-Associated Center (GAC), The Sarcin--Ricin Loop (SRL), and L7/L12 Stalk 341
15.2.3.2 The Exit Site 342
15.2.3.3 Other Ribosomal Protein Mutants 343
15.3 Mutants Affecting Translational Recoding in Eukaryotes 344
15.3.1 Cis-Acting Elements Affecting Translational Recoding 345
15.3.1.1 The Ribosome 345
15.3.1.2 18S rRNA Mutants 345
15.3.1.3 25S rRNA Mutants 346
15.3.1.4 5S rRNA Mutants 347
15.3.1.5 rRNA Base Modification Mutants 347
15.3.1.6 Ribosomal Proteins and Translational Inhibitors 347
15.3.2 Trans-Acting Elements Affecting Translational Recoding 348
15.4 Concluding Comments 350
References 351
16 The E Site and Its Importance for Improving Accuracy and Preventing Frameshifts 358
16.1 Introduction: All Ribosomes Have Three tRNA Binding Sites 358
16.2 Features of the E Site 360
16.3 A Cognate E-tRNA Prevents Misincorporation of Non-cognate Amino Acids 362
16.4 ShineDalgarno Sequence Can Take Over the Function of the E-tRNA 366
16.5 Maintaining the Reading Frame 370
References 371
Part III Discontiguity 376
17 Translational Bypassing Peptidyl-tRNA Re-pairing at Non-overlapping Sites 377
17.1 Introduction 377
17.2 Non-programmed Bypassing 378
17.3 Programmed Bypassing 379
17.4 The UAG Codon Following Take-Off Site 380
17.5 Matched Take-Off and Landing Codons 381
17.6 Peptidyl- 381
17.7 Nascent Peptide Effect 383
17.8 ShineDalgarno Sequence Within the Coding Gap 383
17.9 RNA Structure of the Coding Gap and Landing Fidelity 384
17.10 Ribosomal Protein L9 386
17.11 Model for Gene 60 Bypassing 388
17.12 Significance of Bypassing 390
References 391
18 trans -Translation 394
18.1 Introduction 395
18.2 tmRNASmpB Structure 397
18.3 tmRNA Charging 399
18.4 Interaction with the Ribosome 400
18.5 Proteolysis of Tagged Proteins 401
18.6 Degradation of the Substrate mRNA 402
18.7 Signals for Recoding by trans -Translation 403
18.8 mRNA Cleavage as a Signal for trans -Translation 404
18.9 Regulation of trans -Translation Activity 406
18.10 Physiology of trans -Translation 408
18.11 Stress Phenotypes 409
18.12 Effects on Regulatory Pathways 409
18.13 trans -Translation Effects on Bacterial Development 412
18.14 trans -Translation Effects on Phage Development 412
18.15 Virulence Defects 413
18.16 Role of Proteolysis and Ribosome Release in Bacterial Physiology 413
References 414
Part IV Transcription Slippage 417
19 Transcript Slippage and Recoding 418
19.1 The Phenomenon of Transcript Slippage 419
19.2 Evidence for Transcript Slippage During Elongation In Vivo 420
19.3 Slippage in Viral Systems 424
19.4 Slippage in Nonhomopolymeric Tracts 424
19.5 Transcript Slippage During Initiation 425
19.6 Transcript Slippage During ElongationIn Vitro Studies 426
19.7 Structural and Mechanistic Considerations of Translocation 428
19.8 Molecular Mechanisms of Transcript Slippage 430
19.9 Transcript Slippage During Termination 433
19.10 Concluding Remarks 436
References 437
Part V Appendix 442
20 Computational Resources for Studying Recoding 443
20.1 Recoding in the Genomic Era 444
20.2 Databases of Recoding Events 445
20.2.1 Recode Database 445
20.2.2 Frameshift Database (FSDB) 448
20.2.3 Programmed Ribosomal Frameshifting Database (PRFDB) 450
20.2.4 SelenoDB 450
20.2.5 ISfinder 451
20.3 Approaches and Methods for Finding Recoded Genes 451
20.3.1 Homology Searching 453
20.3.2 Pattern Searching 454
20.3.3 RNA Structure Prediction 456
20.3.4 Coding Potential 458
20.4 Computer Programs Specifically Designed for Finding Recoding Events 459
20.4.1 FSFinder 459
20.4.2 ARFA 460
20.4.3 OAF 461
20.4.4 SECISearch 462
20.4.5 FreqAnalysis 463
20.5 XML Format to Describe Recoding Events 464
References 465
Index 470