Analysis of tetra- and hepta-nucleotides motifs promoting -1 ribosomal frameshifting in Escherichia coli.
Bottom Line: Depending on the signal, the frameshifting frequency can vary over a wide range, from less than 1% to more than 50%.While motif efficiency varies widely, a major distinctive rule of bacterial -1 frameshifting is that the most efficient motifs are those allowing cognate re-pairing of the A site tRNA from ZZN to ZZZ.The outcome of the genomic search is a set of 69 gene clusters, 59 of which constitute new candidates for functional utilization of -1 frameshifting.
Affiliation: School of Biochemistry and Cell biology, University College Cork, Cork, Ireland.Show MeSH
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Mentions: Gene families possibly using these patterns for -1 PRF were identified using the pipeline described in Materials and Methods. This procedure led to 658 alignments which represented gene families with sequences containing one of the 21 chosen X_XX.Z_ZZ.N patterns. Subsequent filtering on the basis frameshift site conservation reduced that number to 69 clusters: 8 correspond to mobile genetic elements, 5 are from prophage genes and 56 belong to other gene families (Supplementary Table S4 and S5). The main features of these 69 clusters are summarized in Figure 8. It appears that the size of the gene containing the frameshift signal is very variable, since it can code for a 44–1426 amino acid protein (Supplementary Table S6, Figure 8A). In 57 clusters, the frameshift product is shorter than the product of normal translation (Supplementary Table S6, Figure 8B). The degree of conservation of synonymous sites around the frameshift site was also analysed (46); Figure 8C (http://lapti.ucc.ie/heptameric_patterns_clusters/). Synonymous sites are supposed to evolve neutrally unless there are additional constraints acting at the nucleotide sequence level, for example, pressure to conserve an RNA structure. Only 2 out of the 56 non-mobile genes display reduced variability at synonymous sites in the vicinity of the frameshift site, whereas 4 IS clusters and 1 prophage cluster do show such suppression (RVSS/alndiv column in Supplementary Tables S4 and S5). However, failure to detect statistically significant synonymous site conservation in the other clusters may be due to insufficient sequence divergence (RVSS/alndiv column in Supplementary Tables S4 and S5). Among the clusters displaying reduced variability, 1 non-mobile cluster (A_AAA_AAG_6), and 3 IS clusters (A_AAA_AAG_2, A_AAA_AAG_3 and A_AAA_AAG_4) possess a proven or potential stimulatory structure downstream of the motif. One IS cluster with reduced variability (A_AAA_AAC_1, a proven case of frameshifting) has no established stimulator (4,53). Two IS clusters do not display reduced synonymous site variability (A_AAA_AAA_1 and A_AAA_AAG_37) in spite of being proven cases where -1 frameshifting is stimulated by a stem-loop structure (unpublished data) (58).
Affiliation: School of Biochemistry and Cell biology, University College Cork, Cork, Ireland.