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Analysis of tetra- and hepta-nucleotides motifs promoting -1 ribosomal frameshifting in Escherichia coli.

Sharma V, Prère MF, Canal I, Firth AE, Atkins JF, Baranov PV, Fayet O - Nucleic Acids Res. (2014)

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.

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Affiliation: School of Biochemistry and Cell biology, University College Cork, Cork, Ireland.

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Overview of the proteins produced by normal translation or by -1 frameshifting for one gene typical of each of the 69 clusters of genes selected on the basis of high conservation of an X_XX.Z_ZZ.N motif in the nrMEG. The selection pipeline is indicated in Materials and Methods and the properties of each cluster are given in Supplementary Table S4–S6. The data of Supplementary Table S6 relative to the size of the protein products were plotted as follows. Panel A shows the size in amino acids of the full-length frame 0 protein as a function of the cluster order presented in the first column of Supplementary Table S6 (clusters were ordered by increasing value of the size ratio between the frameshift product and the frame 0 protein). Panel B, presents the size variation of the -1 frameshift product (circles) and of the normal, frame 0, translation product up to the end of the X_XX.Z_ZZ.N motif (triangles) (all sizes are relative to that of the corresponding full-length frame 0 product) as a function of the cluster order shown in the first column of Supplementary Table S6. The 10 demonstrated cases of frameshifting are indicated on each panel as true PRF-1 and dnaX or IS and phages (details about these clusters can be found in Supplementary Tables S4 and S5). Panel C summarizes qualitatively the features of each of the 69 clusters. Each square represents a cluster, and the features (absence of stimulator, presence of an upstream SD or of a downstream structure, existence of a -1 protein longer than the 0 frame product and demonstration of -1 PRF) are symbolized as indicated below the panel. Clusters in the two upper boxes are those displaying reduced variability at synonymous sites (rvss+; see Materials and Methods, Supplementary Tables S4 and S5) and clusters in the two lower boxes are those without reduced variability (rvss−).
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Figure 8: Overview of the proteins produced by normal translation or by -1 frameshifting for one gene typical of each of the 69 clusters of genes selected on the basis of high conservation of an X_XX.Z_ZZ.N motif in the nrMEG. The selection pipeline is indicated in Materials and Methods and the properties of each cluster are given in Supplementary Table S4–S6. The data of Supplementary Table S6 relative to the size of the protein products were plotted as follows. Panel A shows the size in amino acids of the full-length frame 0 protein as a function of the cluster order presented in the first column of Supplementary Table S6 (clusters were ordered by increasing value of the size ratio between the frameshift product and the frame 0 protein). Panel B, presents the size variation of the -1 frameshift product (circles) and of the normal, frame 0, translation product up to the end of the X_XX.Z_ZZ.N motif (triangles) (all sizes are relative to that of the corresponding full-length frame 0 product) as a function of the cluster order shown in the first column of Supplementary Table S6. The 10 demonstrated cases of frameshifting are indicated on each panel as true PRF-1 and dnaX or IS and phages (details about these clusters can be found in Supplementary Tables S4 and S5). Panel C summarizes qualitatively the features of each of the 69 clusters. Each square represents a cluster, and the features (absence of stimulator, presence of an upstream SD or of a downstream structure, existence of a -1 protein longer than the 0 frame product and demonstration of -1 PRF) are symbolized as indicated below the panel. Clusters in the two upper boxes are those displaying reduced variability at synonymous sites (rvss+; see Materials and Methods, Supplementary Tables S4 and S5) and clusters in the two lower boxes are those without reduced variability (rvss−).

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).


Analysis of tetra- and hepta-nucleotides motifs promoting -1 ribosomal frameshifting in Escherichia coli.

Sharma V, Prère MF, Canal I, Firth AE, Atkins JF, Baranov PV, Fayet O - Nucleic Acids Res. (2014)

Overview of the proteins produced by normal translation or by -1 frameshifting for one gene typical of each of the 69 clusters of genes selected on the basis of high conservation of an X_XX.Z_ZZ.N motif in the nrMEG. The selection pipeline is indicated in Materials and Methods and the properties of each cluster are given in Supplementary Table S4–S6. The data of Supplementary Table S6 relative to the size of the protein products were plotted as follows. Panel A shows the size in amino acids of the full-length frame 0 protein as a function of the cluster order presented in the first column of Supplementary Table S6 (clusters were ordered by increasing value of the size ratio between the frameshift product and the frame 0 protein). Panel B, presents the size variation of the -1 frameshift product (circles) and of the normal, frame 0, translation product up to the end of the X_XX.Z_ZZ.N motif (triangles) (all sizes are relative to that of the corresponding full-length frame 0 product) as a function of the cluster order shown in the first column of Supplementary Table S6. The 10 demonstrated cases of frameshifting are indicated on each panel as true PRF-1 and dnaX or IS and phages (details about these clusters can be found in Supplementary Tables S4 and S5). Panel C summarizes qualitatively the features of each of the 69 clusters. Each square represents a cluster, and the features (absence of stimulator, presence of an upstream SD or of a downstream structure, existence of a -1 protein longer than the 0 frame product and demonstration of -1 PRF) are symbolized as indicated below the panel. Clusters in the two upper boxes are those displaying reduced variability at synonymous sites (rvss+; see Materials and Methods, Supplementary Tables S4 and S5) and clusters in the two lower boxes are those without reduced variability (rvss−).
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Figure 8: Overview of the proteins produced by normal translation or by -1 frameshifting for one gene typical of each of the 69 clusters of genes selected on the basis of high conservation of an X_XX.Z_ZZ.N motif in the nrMEG. The selection pipeline is indicated in Materials and Methods and the properties of each cluster are given in Supplementary Table S4–S6. The data of Supplementary Table S6 relative to the size of the protein products were plotted as follows. Panel A shows the size in amino acids of the full-length frame 0 protein as a function of the cluster order presented in the first column of Supplementary Table S6 (clusters were ordered by increasing value of the size ratio between the frameshift product and the frame 0 protein). Panel B, presents the size variation of the -1 frameshift product (circles) and of the normal, frame 0, translation product up to the end of the X_XX.Z_ZZ.N motif (triangles) (all sizes are relative to that of the corresponding full-length frame 0 product) as a function of the cluster order shown in the first column of Supplementary Table S6. The 10 demonstrated cases of frameshifting are indicated on each panel as true PRF-1 and dnaX or IS and phages (details about these clusters can be found in Supplementary Tables S4 and S5). Panel C summarizes qualitatively the features of each of the 69 clusters. Each square represents a cluster, and the features (absence of stimulator, presence of an upstream SD or of a downstream structure, existence of a -1 protein longer than the 0 frame product and demonstration of -1 PRF) are symbolized as indicated below the panel. Clusters in the two upper boxes are those displaying reduced variability at synonymous sites (rvss+; see Materials and Methods, Supplementary Tables S4 and S5) and clusters in the two lower boxes are those without reduced variability (rvss−).
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).

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.

View Article: PubMed Central - PubMed

Affiliation: School of Biochemistry and Cell biology, University College Cork, Cork, Ireland.

Show MeSH
Related in: MedlinePlus