Structural basis of Cfr-mediated antimicrobial resistance and mechanisms for its evasion

Abstract

The ribosome is an essential drug target as many classes of clinically important antibiotics bind and inhibit its functional centers. The catalytic peptidyl transferase center (PTC) is targeted by the broadest array of inhibitors belonging to several chemical classes. One of the most abundant and clinically prevalent mechanisms of resistance to PTC-acting drugs is C8-methylation of the universally conserved adenine residue 2503 (A2503) of the 23S rRNA by the methyltransferase Cfr. Despite its clinical significance, a sufficient understanding of the molecular mechanisms underlying Cfr-mediated resistance is currently lacking. In this work, we developed a method to express a functionally-active Cfr-methyltransferase in the thermophilic bacteriumThermus thermophilusand report a set of high-resolution structures of the Cfr-modified 70S ribosome containing aminoacyl- and peptidyl-tRNAs. Our structures reveal that an allosteric rearrangement of nucleotide A2062 upon Cfr-methylation of A2503 is likely responsible for the inability of some PTC inhibitors to bind to the ribosome, providing additional insights into the Cfr resistance mechanism. Lastly, by determining the structures of the Cfr-methylated ribosome in complex with the antibiotics iboxamycin and tylosin, we provide the structural bases behind two distinct mechanisms of evading Cfr-mediated resistance.

An antibiotic preorganized for ribosomal binding overcomes antimicrobial resistance

“…To understand how CRM so effectively inhibits the growth of bacterial strains expressing the ribosomal methylase genes cfr and erm , which passivate all other PTC-targeting antibiotics, we determined at 2.55-Å and 2.60-Å resolution, respectively, x-ray crystal structures of CRM bound to methylated 70 S ribosomes isolated from cfr -expressing ( 42 ) and erm -expressing ( 43 ) T. thermophilus strains (figs. S5, C to F).…”