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. 2001 Sep;2(9):787-93.
doi: 10.1093/embo-reports/kve176. Epub 2001 Aug 23.

Impact of the six nucleotides downstream of the stop codon on translation termination

O Namy  1 , I Hatin, J P Rousset
Affiliations

Impact of the six nucleotides downstream of the stop codon on translation termination

O Namy et al. EMBO Rep. 2001 Sep.

Abstract

The efficiency of translation termination is influenced by local contexts surrounding stop codons. In Saccharomyces cerevisiae, upstream and downstream sequences act synergistically to influence the translation termination efficiency. By analysing derivatives of a leaky stop codon context, we initially demonstrated that at least six nucleotides after the stop codon are a key determinant of readthrough efficiency in S. cerevisiae. We then developed a combinatorial-based strategy to identify poor 3' termination contexts. By screening a degenerate oligonucleotide library, we identified a consensus sequence -CA(A/G)N(U/C/G)A-, which promotes >5% readthrough efficiency when located downstream of a UAG stop codon. Potential base pairing between this stimulatory motif and regions close to helix 18 and 44 of the 18S rRNA provides a model for the effect of the 3' stop codon context on translation termination.

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Figures

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Fig. 1. Readthrough visualization. Different readthrough motifs, ranging from 1 to 30%, were introduced in the ADE2 gene cloned into a pFL38 plasmid. These plasmids were used to transform the FS1 strain. Exponentially growing cells were spotted on plates (1 × 106 cells/ml) and colour was checked after 3 days at 30°C.
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Fig. 2. Number of occurrences of each nucleotide in the 3′ sequence. (A) Results of the initial screening. The y-axis represents the number of occurrences at positions +4, +5, +6, +7, +8 and +9. (B) Only sequences giving readthrough values >5% were taken into account. (C) Expected frequencies of nucleotides at +4 to +9 positions from natural stop codons in the yeast genome. Results were obtained from the Transterm database (Jacobs et al., 2000).
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Fig. 3. Possible pairing between the 3′ readthrough motif and 18S rRNA. (A) Pairing with helix 17. (B) Pairing with the 1310 region. (•) Non-conventional base pairing.
See this image and copyright information in PMC

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