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Previous studies have shown that the guanine plus cytosine (G+C) content of ribosomal RNAs (rRNAs) is highly correlated with bacterial growth temperatures. This correlation is strongest in the double-stranded stem regions of the rRNA, a fact that can be explained by selection for increased structural stability at high growth temperatures. In this study, we examined the single-stranded regions of 16S rRNAs. We reasoned that, since these regions of the molecule are subject to less structural constraint than the stem regions, their nucleotide content might simply reflect the overall nucleotide content of the genome. Contrary to this expectation, however, we found that all of the single-stranded regions are characterized by very high adenine (A) and relatively low cytosine (C) contents. Moreover, the nucleotide content of these single-stranded regions is surprisingly constant between species, despite dramatic differences in optimal growth temperatures, and despite large differences in the overall genomic G+C content. This provides compelling evidence for strong stabilizing selection acting on 16S rRNA single-stranded regions. We found that selection favors purines (A+G), and especially adenine (A), in the single-stranded regions of these rRNAs.

Evidence for strong selective constraint acting on the nucleotide composition of 16S ribosomal RNA genes