Programmed Alternative Reading of the Genetic Code: by Philip J. Farabaugh

By Philip J. Farabaugh

2. The Translational equipment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . five Translation Initiation in Prokaryotes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 Translation Initiation in Eukaryotes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . eight 14 Translation Elongation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Translation Termination in Prokaryotes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . sixteen Translation Termination in Eukaryotes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17 mistakes Correction in Translation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18 A Structural foundation of mistakes Correction in Translation . . . . . . . . . . . . . . . . . . . . . . . . . . 20 Ribosome modifying: A Failsafe blunders Correction Mechanism . . . . . . . . . . . . . . . . 22 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22 three. error in the course of Elongation may cause Translational 29 Frameshifting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Spontaneous Frameshifting as opposed to Programmed Frameshifting . . . . . . . . . . 30 Spontaneous Frameshifts may be brought about at particular Codons . . . . . . . . . . . . 31 four. Programmed ]1 Frameshifting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . forty-one The pifE Gene of E. coli . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . forty-one utilizing the pifE method to check basic Frameshifting in E. coli . . . . . . . . forty six Ty Retrotransposons in Yeast . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . forty seven Frameshifting in Retrotransposon Ty1 happens through tRNA Slippage . . . . . . . forty eight Frameshifting in Retrotransposon Ty3 happens by way of Out-of-Frame Binding of tRNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . fifty one The Rat Ornithine Decarboxylase Antizyme Gene . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . fifty six precis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . sixty two five. Programmed -1 Frameshifting in Eukaryotes . . . . . . . . . . . . . . . . . . . . . . . . . . . sixty nine Programmed -1 Frameshifting in Eukaryotes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . sixty nine -1 Frameshifting happens on a "Slippery Heptamer" . . . . . . . . . . . . . . . . . . . . . . . . . . . seventy one The Simultaneous-Slippage version . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . seventy two of -1 Frameshifting through a Downstream Pseudoknot . . . . . . . . . . seventy seven Stimulation Does the Pseudoknot basically Block Passage of the Ribosome? . . . . . . . . . .

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Proc Natl Acad Sci USA 1989; 86:3119-22. 27 79. Zhang Y, Dolph PJ, Schneider RJ. Secondary structure analysis of adenovirus tripartite leader. J BioI Chern 1989; 264:10679-84. 80. Zhouravleva G, Frolova L, Le Goff X, Le Guellec R, Inge-Vechtomov S, Kisselev L, Philippe M. Termination of translation in eukaryotes is governed by two interacting polypeptide chain release factors, eRF1 and eRF3. EMBO J 1995; 14:4065-4072. ====CHAPTER3==== ERRORS DURING ELONGATION CAN CAUSE TRANSLATIONAL FRAMESHIFTING I n general, the translational machinery more efficiently eliminates frameshift errors than any other sort.

Out of frame decoding appears to depend on the identity of both the peptidyl-tRNA in the P site and of the aminoacyl-tRNA which must enter the ribosome in the + 1 frame. The third mechanism involves slippage of peptidyl-tRNA from its cognate codon onto a near cognate codon. In this case, slippage depends at a minimum on the redundant sequence of the nucleotides in the mRNA, though the requirement for some structure in the tRNA undergoing slippage has not been eliminated. In each of these paradigms a normally forbidden event occurs which results in frameshifting.

Pulling the ribosome out of frame + 1 at a 21. 22. 23. 24. 25. 26. 27. 28. 29. 30. 39 programmed frameshift site by cognate binding of aminoacyl-tRNA. Mol Cell BioI 1995; 15 :298-304. Peter K, Lindsley D, Peng L et al. Context rules of rightward overlapping reading. New BioI 1992; 4:520-526. Quigley GJ, Rich A. Structural domains of transfer RNA molecules. Science 1976; 194: 796-806. Riddle D, Carbon J. Frameshift suppression: a nucleotide addition in the anticodon of a glycine tRNA. Nature New BioI 1973; 242:230-234.

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