Methods to Analyze Post-transcriptional Modifications Applied to Stable RNAs in Staphylococcus aureus

RNA modifications contribute to the various functions of RNAs in all living organisms. Some of these modifications are dynamic and contribute to the regulation of gene expression. In bacteria, their roles in stress, environmental adaptation, and in infections caused by pathogens have been recently fully recognized. In this review, we describe several methodologies including mass spectrometry, next-generation RNA sequencing methods, biochemical approaches, and cryo-EM structural analysis that are used to detect and localize the modifications in tRNAs and rRNAs. We illustrate how the combination of methods was necessary to avoid technical biases for a successful mapping of the modifications in tRNAs and rRNAs in Staphylococcus aureus.