How Changes in Anti-SD Sequences Would Affect SD Sequences in Escherichia coli and Bacillus subtilis

The 3′ end of the small ribosomal RNAs (ssu rRNA) in bacteria is directly involved in the selection and binding of mRNA transcripts during translation initiation via well-documented interactions between a Shine-Dalgarno (SD) sequence located upstream of the initiation codon and an anti-SD (aSD) sequence at the 3′ end of the ssu rRNA. Consequently, the 3′ end of ssu rRNA (3′TAIL) is strongly conserved among bacterial species because a change in the region may impact the translation of many protein-coding genes. Escherichia coli and Bacillus subtilis differ in their 3′ ends of ssu rRNA, being GAUCACCUCCUUA3′ in E. coli and GAUCACCUCCUUUCU3′ or GAUCACCUCCUUUCUA3′ in B. subtilis. Such differences in 3′TAIL lead to species-specific SDs (designated SD(Ec) for E. coli and SD(Bs) for B. subtilis) that can form strong and well-positioned SD/aSD pairing in one species but not in the other. Selection mediated by the species-specific 3′TAIL is expected to favor SD(Bs) against SD(Ec) in B. subtilis, but favor SD(Ec) against SD(Bs) in E. coli. Among well-positioned SDs, SD(Ec) is used more in E. coli than in B. subtilis, and SD(Bs) more in B. subtilis than in E. coli. Highly expressed genes and genes of high translation efficiency tend to have longer SDs than lowly expressed genes and genes with low translation efficiency in both species, but more so in B. subtilis than in E. coli. Both species overuse SDs matching the bolded part of the 3′TAIL shown above. The 3′TAIL difference contributes to the host specificity of phages.