A novel insight in favor of structure-function relationship for 16S rRNA.

Sequences in the stem-loop part of 16S ribosomal RNA (rRNA) are considered to be crucial for predicting antibiotic resistance. Mutant sequences have been reported to be helpful in the prediction of spectinomycin resistance. It is expected that such mutations alter the 16S rRNA stem-loop conformation, which affects antibiotic binding. Metagenomic database provides 16S ribosomal DNA sequences isolated from environmental samples. Using in silico tools, we observed that the existence of specific mutation does not alter the stem-loop structure of 16S rRNA along with its three-dimensional conformation. Our observation suggests that the three-dimensional structure is a better guide to understand whether a specific mutation can cause spectinomycin resistance.