Conformational plasticity across phylogenetic clusters of RND multidrug efflux pumps and its impact on substrate specificity
Antibiotic efflux plays a key role for the multidrug resistance in Gram-negative bacteria. Multidrug efflux pumps of the resistance nodulation and cell division (RND) superfamily function as part of cell envelope spanning systems and provide resistance to diverse antibiotics. Here, we identify two phylogenetic clusters of RND proteins with conserved binding pocket residues and show that the transfer of a single conserved residue between both clusters affects the resistance phenotype not only due to changes in the physicochemical properties of the binding pocket, but also due to an altered equilibrium between the conformational states of the transport cycle. We demonstrate, using single-particle cryo-electron microscopy, that AcrB and OqxB, which represent both clusters, adopt fundamentally different apo states, implying distinct mechanisms for initial substrate binding. The observed conformational plasticity appears phylogenetically conserved and likely plays a role in the diversification of the resistance phenotype among homologous RND pumps.
Authors
- Mariya Lazarova
- Mohd Athar (ORCID: https://orcid.org/0000-0001-6337-1026)
- Eiki Yamashita (ORCID: https://orcid.org/0000-0002-4278-0039)
- Kay Diederichs (ORCID: https://orcid.org/0000-0001-5360-0905)
- Satoshi Murakami (ORCID: https://orcid.org/0000-0001-5553-7663)
- Hi-jea Cha
- Attilio Vittorio Vargiu (ORCID: https://orcid.org/0000-0003-4013-8867)
- Ui Okada (ORCID: https://orcid.org/0000-0001-7633-9308)
- Thomas Eicher
- Klaas M. Pos (ORCID: https://orcid.org/0000-0001-9035-3827)
- Clara Börnsen (ORCID: https://orcid.org/0009-0002-5547-6789)
- Hui Zeng (ORCID: https://orcid.org/0009-0007-2578-4090)
- Achilleas S Frangakis (ORCID: https://orcid.org/0000-0002-4364-6202)
- Inga M. Spannaus
- Max Borgosch
Institutions
- Goethe University Frankfurt (DE)
- Tokyo Institute of Technology (JP)
- University of Cagliari (IT)
- University of Konstanz (DE)
- Max Planck Institute of Biophysics (DE)
- Protein Research Foundation (JP)
- The University of Osaka (JP)
Publication Details
- Journal
- Nature Communications
- Published
- 2025-11-26
- DOI
- https://doi.org/10.1038/s41467-025-66751-3
- Citations
- 1
- Primary Topic
- Antibiotic Resistance in Bacteria
- Type
- article
- Field-Weighted Citation Impact
- 0.59
Funders
- Pfizer
- Japan Agency for Medical Research and Development
- Università degli Studi di Cagliari
- European Commission
- Deutsche Forschungsgemeinschaft
- National Institutes of Health
- Japan Society for the Promotion of Science
- Institute for Protein Research, Osaka University
- National Institute of Allergy and Infectious Diseases