Figure 4.

aSD binding scores negatively correlate with gene expression in E. coli. (A) An example dataset showing negative correlation between protein abundance and aSD (anti- Shine-Dalgarno) binding scores for individual E. coli genes ($R_{\mathrm{adj}}^2=0.175,$ $p<{10}^{-18}$). Specifically, coding sequences containing fewer SD sequence motifs have higher protein abundances. (B) Multivariate regression shows that expression changes cannot be fully explained by codon usage bias, and that additional predictive power is offered by $S_{\mathrm{gene}}.$ We chose five datasets that provide independent measurements of mRNA (messenger RNA), protein, and translation efficiency levels in order to test the robustness of our findings (Lu et al. 2007; Taniguchi et al. 2010; Shiroguchi et al. 2012; Li et al. 2014).