How changes in anti-SD sequences would affect SD sequences in Escherichia coli and Bacillus subtilis

Abstract

The 39 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 39 end of the ssu rRNA. Consequently, the 39 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 39 ends of ssu rRNA, being GAUCACCUCCUUA39 in E. coli and GAUCACCUCCUUUCU39 or GAUCACCUCCUUUCUA39 in B. subtilis. Such differences in 3'TAIL lead to species-specific SDs (designated SDEc for E. coli and SDBs 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 speciesspecific 3'TAIL is expected to favor SDBs against SDEc in B. subtilis, but favor SDEc against SDBs in E. coli. Among well-positioned SDBs, SDEc is used more in E. coli than in B. subtilis, and SDBs 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.