Structure of Erm-modified 70S ribosome reveals the mechanism of macrolide resistance

Nat Chem Biol. 2021 Apr;17(4):412-420. doi: 10.1038/s41589-020-00715-0. Epub 2021 Jan 18.

Abstract

Many antibiotics inhibit bacterial growth by binding to the ribosome and interfering with protein biosynthesis. Macrolides represent one of the most successful classes of ribosome-targeting antibiotics. The main clinically relevant mechanism of resistance to macrolides is dimethylation of the 23S rRNA nucleotide A2058, located in the drug-binding site, a reaction catalyzed by Erm-type rRNA methyltransferases. Here, we present the crystal structure of the Erm-dimethylated 70S ribosome at 2.4 Å resolution, together with the structures of unmethylated 70S ribosome functional complexes alone or in combination with macrolides. Altogether, our structural data do not support previous models and, instead, suggest a principally new explanation of how A2058 dimethylation confers resistance to macrolides. Moreover, high-resolution structures of two macrolide antibiotics bound to the unmodified ribosome reveal a previously unknown role of the desosamine moiety in drug binding, laying a foundation for the rational knowledge-based design of macrolides that can overcome Erm-mediated resistance.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Anti-Bacterial Agents / pharmacology
  • Drug Resistance, Bacterial / genetics
  • Macrolides / metabolism*
  • Macrolides / pharmacology
  • Methylation
  • RNA, Ribosomal / genetics
  • RNA, Ribosomal / ultrastructure*
  • RNA, Ribosomal, 23S / genetics
  • RNA, Ribosomal, 23S / metabolism
  • RNA, Ribosomal, 23S / ultrastructure
  • Ribosomes / genetics
  • Ribosomes / metabolism
  • Ribosomes / ultrastructure*

Substances

  • Anti-Bacterial Agents
  • Macrolides
  • RNA, Ribosomal
  • RNA, Ribosomal, 23S