3′ Terminal sequences of 16S rRNA do not explain translational specificity differences between E. coli and B. stearothermophilus ribosomes

Abstract

DIRECT Watson–Crick base pairing between the 3′ terminus of 16S RNA and messenger RNA seems to contribute to the recognition and binding of protein synthesis initiator regions by Escherichia coli^1,2. Since bacterial species differ in the pyrimidine-rich sequences at the 3′ termini of their 16S RNAs, it has been suggested that this mRNA–rRNA interaction can account for observed differences in translational specificity among prokaryotes³. To test this hypothesis, we have asked whether it explains the choice of sites bound by Bacillus stearothermophilus ribosomes in two mRNAs—the R17 and Qβ phage genomes. The RNA sequence data presented here lead to two conclusions. First, B. stearothermophilus ribosome recognition of two non-initiator Qβ regions at high temperature⁴ is indeed correlated with an extensive mRNA–rRNA match. Second, surprisingly, the 3′ terminal sequence of 16S rRNA from B. stearothermophilus is identical to that of E. coli^1,5–7 except that the 3′ terminal adenosine of E. coli rRNA is replaced by UCUA_OH in the thermophile. Thus, rRNA sequences at the 3′ end of 16S rRNA cannot explain differences in the capacity of ribosomes from these two species to recognise RNA phage initiator regions at lower temperatures^4,8,9.