RNA modification and antibiotic resistance

Increasing global spread of antibiotic resistance among pathogenic bacteria threatens a post-antibiotic era in healthcare. Detailed studies of resistance mechanisms are therefore urgently required. The ribosome is a major antibiotic target, but bacteria can acquire resistance by modification of drug-binding sites. In collaboration with Prof. Graeme Conn’s lab at Emory University, we have been studying the molecular basis for antibiotic-resistance arising via enzymatic modification of the small ribosomal subunit. We solved the X-ray structure of the first molecular ‘snapshot’ of 30S recognition by a human pathogen-derived, aminoglycoside-resistance rRNA methyltransferase, NpmA (Dunkle et al., PNAS 2014).

Figure 4Surprisingly NpmA modifies its target 16S rRNA nucleotide, A1408, by flipping the nucleotide out of its RNA helix, despite space for NpmA to access the base edge (Figure 4). Though it had been originally proposed that these enzymes were acquired by human and animal pathogens, they share low sequence identity with enzymes from producer bacteria such as actinomycetes. Therefore it is an open question whether these pathogen enzymes were acquired from producers or whether they arose by convergent evolution.

Future experiments include determining how structurally dissimilar but functionally equivalent methyltransferases recognize the 30S ribosomal subunit. Our initial studies indicate that subtle differences in methyltransferase residues that direct recognition of 30S have a direct result in whether the enzyme is preloaded with its obligate SAM cofactor or whether the ribosome plays a role in recycling the reaction by-product SAH for SAM while the methyltransferase is bound to the ribosome.

  • Dunkle JA, Vinnal K, Desai PM, Zelinskaya N, Savic M, West DM, Conn GL* and Dunham CM*. (2014) Molecular recognition and modification of the 30S ribosome by the aminoglycoside-resistance methyltransferase NpmA. Proc Natl Acad Sci 111(17):6275-80. PMCID: PMC4035980. [*Co-corresponding authors] (abstract)