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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
Léa 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-Françoise Prère 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, Michaël Bekaert, Pavel V. Baranov Appendix
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
Léa 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-Françoise Prère 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, Michaël Bekaert, Pavel V. Baranov Appendix
Redefinition.- Selenocysteine Biosynthesis, Selenoproteins, and Selenoproteomes.- Reprogramming the Ribosome for Selenoprotein Expression: RNA Elements and Protein Factors.- Translation of UAG as Pyrrolysine.- Specification of Standard Amino Acids by Stop Codons.- Ribosome “Skipping”: “Stop-Carry On” or “StopGo” Translation.- Recoding Therapies for Genetic Diseases.- Frameshifting – Redirection of Linear Readout.- Pseudoknot-Dependent Programmed —1 Ribosomal Frameshifting: Structures, Mechanisms and Models.- Programmed —1 Ribosomal Frameshift in the Human Immunodeficiency Virus of Type 1.- Ribosomal Frameshifting in Decoding Plant Viral RNAs.- Programmed Frameshifting in Budding Yeast.- Recoding in Bacteriophages.- Programmed Ribosomal ?1 Frameshifting as a Tradition: The Bacterial Transposable Elements of the IS3 Family.- Autoregulatory Frameshifting in Antizyme Gene Expression Governs Polyamine Levels from Yeast to Mammals.- Sequences Promoting Recoding Are Singular Genomic Elements.- Mutants That Affect Recoding.- The E Site and Its Importance for Improving Accuracy and Preventing Frameshifts.- Discontiguity.- Translational Bypassing – Peptidyl-tRNA Re-pairing at Non-overlapping Sites.- trans-Translation.- Transcription Slippage.- Transcript Slippage and Recoding.- Computational Resources for Studying Recoding.
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