Skip to main content
. 2016 Sep 20;5:e13479. doi: 10.7554/eLife.13479

Figure 3. The most under-represented mRNA:rRNA interactions correspond to exterior regions of the ribosome.

(A) In the upper bar, the regions of the T. thermophilus SSU rRNA that are under-represented in stable interactions with mRNAs (p<0.05) are highlighted in red. In the lower bar, the inaccessible residues (<3.4 Angstroms from other nucleotides or amino acids in the PDB structure 4WZO). (B) The 3 dimensional structure of the T. thermophilus ribosome includes 5S, SSU and LSU rRNA, 48 ribosomal proteins, 4 tRNA and a bound mRNA (PDB ID: 4WZO) (Rozov et al., 2015). We have highlighted the most avoided regions of the SSU rRNA in red (based upon the fewest stable interactions with T. thermophilus mRNAs (p<0.05). Two different orientations are shown on the left and right, the upper structure shows just the SSU rRNA and mRNA structures, the lower includes the ribosomal proteins (coloured blue). Bottom right, a view of the ribosome that also includes the LSU rRNA (green) is also shown. There is a significant correspondence between the accessibility of a region of SSU rRNA and the degree to which it is avoided (p=2.5 × 10−17, Fisher’s exact test).

DOI: http://dx.doi.org/10.7554/eLife.13479.012

Figure 3.

Figure 3—figure supplement 1. Avoidance pattern and its correlation with protein expression vary on mRNAs.

Figure 3—figure supplement 1.

(A) A sliding window (length 21, step size 1) analysis based on previously published GFP expression dataset (Kudla et al., 2009) shows the significance of the correlation between avoidance and their corresponding fluorescence values for each position along with the coding region. Darker red regions show more significant positions (with higher −log10(P) values). (B) This analysis proves that the binding energy of first 21 nt region influences protein expression more than any other downstream region and corresponding Spearman’s correlation coefficients for selected sliding window start positions are seen at bottomright. It also justifies our selection of 5´ end coding region for avoidance.
DOI: http://dx.doi.org/10.7554/eLife.13479.013

Figure 3—figure supplement 2. Comparison of different regions for evolutionary conservation analyses.

Figure 3—figure supplement 2.

(A) This box and whisker plot (similar to Figure 1C except archaea) shows −log10(P) distributions for each bacterial phylum. The black dashed line indicates the significance threshold (p<0.05). We used 5´ end CDS regions as designated interaction location. (B) In this plot, 5´ end UTR regions (90 nucleotides upstream to 21 nucleotides downstream) are used as designated interaction regions. It seems both regions have similar avoidance conservation, which proves avoidance is not limited to 5´ ends of the coding region.
DOI: http://dx.doi.org/10.7554/eLife.13479.014

Figure 3—figure supplement 3. The most avoided regions of selected T. thermophilus non-coding RNAs.

Figure 3—figure supplement 3.

(A) A graphical view for an alignment of the T. thermophilus tRNAs (n = 46). Regions that have significantly (p<0.001, Mann-Whitney U test) fewer than expected interactions with T. thermophilus mRNAs are highlighted in red. These regions are therefore the most avoided regions by the host’s mRNAs. The grey blocks show gaps in the alignment. (B–D) A graphical view of the most avoided regions is illustrated for tmRNA, RNase P and SRP RNA respectively.
DOI: http://dx.doi.org/10.7554/eLife.13479.015