NMR characterisation of the antibiotic resistance-mediating 32mer RNA from the 23S ribosomal RNA

The increasing prevalence of antibiotic resistance represents a significant public health concern, underscoring the urgent need for the development of novel therapeutic strategies. The antibiotic effects of macrolides, the second most widely used class of antibiotics, are counteracted by Erm proteins through the methylation of adenosine 2058 of the 23S ribosomal RNA (rRNA) (~ 2900 nucleotides), yielding either monomethylated or dimethylated A2058. This methylation is the molecular basis for preventing macrolides from binding and leads to the development of resistance of bacteria including Staphylococcus, Streptococcus and Enterococcus. While the function of Erm proteins have been thoroughly investigated, the role of the ribosomal RNA in acquiring antibiotic resistance is frequently underestimated, given that the ribosomal RNA is the actual target for methylation. Here, we present the comprehensive ¹H, ¹³C and ¹⁵N NMR resonance assignment for the part of the 23S rRNA that serves as the Erm substrate in antimicrobial resistance. Furthermore, we compare the chemical shift signature of the unmethylated to the monomethylated and dimethylated RNA construct and show that changes in the RNA upon methylation are locally restricted. The resonance assignments provide a starting point for investigating and targeting the molecular mechanism of the resistance-conferring Erm proteins.