Philip J. Farabaugh

Programmed Alternative Reading of the Genetic Code: Molecular Biology Intelligence Unit Philip J. Farabaugh 1997 edition

2. 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 ...7 2 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 ...91 Frameshifting Regulates a Morphogenetic Process ...92 6. Programmed -1 Frameshift Sites in Prokaryotes ...103 The dnaXGene: -1 Frameshifting Stimulated by Both Upstream and Downstream Elements ...103 Programmed -1 Frameshifts in Insertion Sequences Are Mechanistically Diverse ...