Recoding: Expansion of Decoding Rules Enriches Gene Expression, Vol. 24 Book

Part I Redefinition

1 Selenocysteine Biosynthesis, Selenoproteins, and Selenoproteomes Vadim N. Gladyshev Dolph L. Hatfield 3

2 Reprogramming the Ribosome for Selenoprotein Expression: RNA Elements and Protein Factors Maria J. Berry Michael T. Howard 29

3 Translation of UAG as Pyrrolysine Joseph A. Krzycki 53

4 Specification of Standard Amino Acids by Stop Codons Olivier Namy Jean-Pierre Rousset 79

5 Ribosome "Skipping": "Stop-Carry On" or "StopGo" Translation Jeremy D. Brown Martin D. Ryan 101

6 Recoding Therapies for Genetic Diseases Kim M. Keeling David M. Bedwell 123

Part II Frameshifting - Redirection of Linear Readout

7 Pseudoknot-Dependent Programmed -1 Ribosomal Frameshifting: Structures, Mechanisms and Models Ian Brierley Robert J.C. Gilbert Simon Pennell 149

8 Programmed -1 Ribosomal Frameshift in the Human Immunodeficiency Virus of Type 1 Léa Brakier-Gingras Dominic Dulude 175

9 Ribosomal Frameshifting in Decoding Plant Viral RNAs W. Allen Miller David P. Giedroc 193

10 Programmed Frameshifting in Budding Yeast Philip J. Farabaugh 221

11 Recoding in Bacteriophages Roger W. Hendrix 249

12 Programmed Ribosomal -1 Frameshifting as a Tradition: The Bacterial Transposable Elements of the IS3 Family Olivier Fayet Marie-Françoise Prère 259

13 Autoregulatory Frameshifting in Antizyme Gene Expression Governs Polyamine Levels from Yeast to Mammals Ivaylo P. Ivanov Senya Matsufuji 281

14 Sequences Promoting Recoding Are Singular Genomic Elements Pavel V. Baranov Olga Gurvich 301

15 Mutants That Affect Recoding Jonathan D. Dinman Michael O'Connor 321

16 The E Site and Its Importance for Improving Accuracy and Preventing FrameshiftsMarkus Pech Oliver Vesper Hiroshi Yamamoto Daniel N. Wilson Knud H. Nierhaus 345

Part III Discontiguity

17 Translational Bypassing - Peptidyl-tRNA Re-pairing at Non-overlapping Sites Norma M. Wills 365

18 trans-Translation Kenneth C. Keiler Dennis M. Lee 383

Part IV Transcription Slippage

19 Transcript Slippage and Recoding Michael Anikin Vadim Molodtsov Dmitry Temiakov William T. McAllister 409

Part V Appendix

20 Computational Resources for Studying Recoding Andrew E. Firth Michaël Bekaert Pavel V. Baranov 435

Index 463