Recoding: Expansion of Decoding Rules Enriches Gene Expression (Nucleic Acids and Molecular Biology)

The literature on recoding is scattered, so this superb book ?lls a need by prov- ing up-to-date, comprehensive, authoritative reviews of the many kinds of recoding phenomena. Between 1961 and 1966 my colleagues and I deciphered the genetic code in Escherichia coli and showed that the genetic code is the same in E. coli, Xenopus laevis, and guinea pig tissues. These results showed that the code has been c- served during evolution and strongly suggested that the code appeared very early during biological evolution, that all forms of life on earth descended from a c- mon ancestor, and thus that all forms of life on this planet are related to one another. The problem of biological time was solved by encoding information in DNA and retrieving the information for each new generation, for it is easier to make a new organism than it is to repair an aging, malfunctioning one. Subsequently, small modi?cations of the standard genetic code were found in certain organisms and in mitochondria. Mitochondrial DNA only encodes about 10-13 proteins, so some modi?cations of the genetic code are tolerated that pr- ably would be lethal if applied to the thousands of kinds of proteins encoded by genomic DNA. Table of Contents Foreword Marshall Nirenberg Preface John F. Atkins, Raymond F. Gesteland Selenocysteine Biosynthesis, Selenoproteins and Selenoproteomes Vadim N. Gladyshev, Dolph L. Hatfield Reprogramming the Ribosome for Selenoprotein Expression: RNA Elements and Protein Factors Marla J. Berry, Michael T. Howard Translation of UAG as pyrrolysine Joseph A. Krzycki Specification of standard amino acids by stop codons Olivier Namy, Jean-Pierre Rousset Ribosome 'Skipping': 'Stop-Carry On' or 'StopGo' Translation Jeremy D. Brown, Martin D. Ryan Recoding Therapies for Genetic Diseases Kim M. Keeling, David M. Bedwell Pseudoknot-dependent Programmed -1 Ribosomal Frameshifting: Structures, Mechanisms and Models Ian Brierley, Robert J. C. Gilbert, Simon Pennell Programmed -1 ribosomal frameshift in the human immunodeficiency virus of type 1 La Brakier-Gingras, Dominic Dulude Ribosomal frameshifting in decoding plant viral RNAs W. Allen Miller, David P. Giedroc Programmed frameshifting in budding yeast Philip J. Farabaugh Recoding in bacteriophages Roger W. Hendrix Programmed Ribosomal -1 Frameshifting as a Tradition: the Bacterial Transposable Elements of the IS3 Family Olivier Fayet, Marie-Franoise Prre Autoregulatory frameshifting in antizyme gene expression governs polyamine levels from yeast to mammals Ivaylo P. Ivanov, Senya Matsufuji Sequences promoting Recoding are Singular Genomic Elements Pavel V.Baranov, Olga Gurvich Mutants that affect recoding Jonathon D. Dinman, Michael O'Connor The E site and its importance for improving accuracy and preventing frameshifts Markus Pech, Oliver Vesper, Hiroshi Yamamoto, Daniel N. Wilson, Knud H. Nierhaus Translational Bypassing - peptidyl-tRNA re-paring at non-overlapping sites Norma M. Wills trans-Translation Kenneth Keiler, Dennis M. Lee Transcript slippage and recoding Michael Anikin, Vadim Molodtsov, Dmitry Temiakov, William T. McAllister Computational resources for studying recoding Andrew E. Firth, Michal Bekaert, Pavel V. Baranov Appendix