Programmed Alternative Reading of the Genetic Code

The Translational Machinery . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 Translation Initiation in Prokaryotes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 Translation Initiation in Eukaryotes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 14 Translation Elongation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Translation Termination in Prokaryotes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16 Translation Termination in Eukaryotes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17 Error Correction in Translation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18 A Structural Basis of Error Correction in Translation . . . . . . . . . . . . . . . . . . . . . . . . . . 20 Ribosome Editing: A Failsafe Error Correction Mechanism . . . . . . . . . . . . . . . . 22 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22 3. Errors During Elongation Can Cause Translational 29 Frameshifting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Spontaneous Frameshifting Versus Programmed Frameshifting . . . . . . . . . . 30 Spontaneous Frameshifts Can Be Induced at Specific Codons . . . . . . . . . . . . 31 4. Programmed +1 Frameshifting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41 The pifE Gene of E. coli . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41 Using the pifE System to Study General Frameshifting in E. coli . . . . . . . . 46 Ty Retrotransposons in Yeast . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47 Frameshifting in Retrotransposon Ty1 Occurs by tRNA Slippage . . . . . . . 48 Frameshifting in Retrotransposon Ty3 Occurs by Out-of-Frame Binding of tRNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51 The Rat Ornithine Decarboxylase Antizyme Gene . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62 5. Programmed -1 Frameshifting in Eukaryotes . . . . . . . . . . . . . . . . . . . . . . . . . . . 69 Programmed -1 Frameshifting in Eukaryotes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69 -1 Frameshifting Occurs on a "Slippery Heptamer" . . . . . . . . . . . . . . . . . . . . . . . . . . . 71 The Simultaneous-Slippage Model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72 of -1 Frameshifting by a Downstream Pseudoknot . . . . . . . . . . 77 Stimulation Does the Pseudoknot Only Block Passage of the Ribosome? . . . . . . . . . . . . . . . 79 Not All Pseudoknots Which Cause Ribosomes to Pause Can Stimulate -1 Frameshifting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84 Is There a Pseudoknot Recognizing Factor? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88 Some Simultaneous-Slippage Sites Do Not Include a Stimulatory Pseudo knot . . . . . .

Klappentext

This book describes the phenomenology of several related unusual events which occur during protein expression from genes which include special sequences. These events, termed programmed alternative coding events, occur ubiquitously, including the AIDS retrovirus. The author explains the mechanisms underlying these unusual events in a large variety of genes, as well as the implications for gene expression in general, and carcinogenesis in particular.

Inhalt

Introduction.- 2. The Translational Machinery.- 3. Errors During Elongation Can Cause Translational Frameshifting.- 4. Programmed +1 Frameshifting.- 5. Programmed ?1 Frameshifting in Eukaryotes.- 6. Programmed ?1 Frameshift Sites in Prokaryotes.- 7. tRNA Hopping.- 8. Programmed Readthrough of Translational Termination Codons.- 9. Programmed Alternative Decoding as Programmed Translational Errors.- 10. Concluding Remarks.