Structural basis of ABCF-mediated resistance to pleuromutilin, lincosamide, and streptogramin A antibiotics in Gram-positive pathogens

Nat Commun. 2021 Jun 11;12(1):3577. doi: 10.1038/s41467-021-23753-1.

Abstract

Target protection proteins confer resistance to the host organism by directly binding to the antibiotic target. One class of such proteins are the antibiotic resistance (ARE) ATP-binding cassette (ABC) proteins of the F-subtype (ARE-ABCFs), which are widely distributed throughout Gram-positive bacteria and bind the ribosome to alleviate translational inhibition from antibiotics that target the large ribosomal subunit. Here, we present single-particle cryo-EM structures of ARE-ABCF-ribosome complexes from three Gram-positive pathogens: Enterococcus faecalis LsaA, Staphylococcus haemolyticus VgaALC and Listeria monocytogenes VgaL. Supported by extensive mutagenesis analysis, these structures enable a general model for antibiotic resistance mediated by these ARE-ABCFs to be proposed. In this model, ABCF binding to the antibiotic-stalled ribosome mediates antibiotic release via mechanistically diverse long-range conformational relays that converge on a few conserved ribosomal RNA nucleotides located at the peptidyltransferase center. These insights are important for the future development of antibiotics that overcome such target protection resistance mechanisms.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • ATP-Binding Cassette Transporters / chemistry
  • ATP-Binding Cassette Transporters / genetics
  • ATP-Binding Cassette Transporters / metabolism
  • Adhesins, Bacterial / chemistry
  • Adhesins, Bacterial / genetics
  • Anti-Bacterial Agents / pharmacology*
  • Bacterial Proteins / chemistry
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Binding Sites
  • Cryoelectron Microscopy
  • Diterpenes / pharmacology*
  • Drug Resistance, Bacterial / drug effects*
  • Drug Resistance, Bacterial / genetics
  • Gram-Positive Bacteria / drug effects*
  • Gram-Positive Bacteria / genetics
  • Lincosamides / pharmacology*
  • Models, Molecular
  • Peptidyl Transferases / metabolism
  • Pleuromutilins
  • Polycyclic Compounds / pharmacology*
  • Protein Conformation
  • RNA, Messenger
  • Ribosomes / metabolism
  • Streptogramins / pharmacology*

Substances

  • ATP-Binding Cassette Transporters
  • Adhesins, Bacterial
  • Anti-Bacterial Agents
  • Bacterial Proteins
  • Diterpenes
  • Lincosamides
  • Polycyclic Compounds
  • RNA, Messenger
  • Streptogramins
  • Peptidyl Transferases