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Structural basis for antibiotic resistance mediated by the Bacillus subtilis ABCF ATPase VmlR

Crowe-McAuliffe, Caillan ; Graf, Michael ; Huter, Paul ; Takada, Hiraku ; Abdelshahid, Maha ; Nováček, Jirí ; Murina, Victoriia ; Atkinson, Gemma C. LU ; Гaврилюк, Bacилий LU orcid and Wilson, Daniel N. (2018) In Proceedings of the National Academy of Sciences of the United States of America 115(36). p.8978-8983
Abstract

Many Gram-positive pathogenic bacteria employ ribosomal protection proteins (RPPs) to confer resistance to clinically important antibiotics. In Bacillus subtilis, the RPP VmlR confers resistance to lincomycin (Lnc) and the streptogramin A (SA) antibiotic virginiamycin M (VgM). VmlR is an ATP-binding cassette (ABC) protein of the F type, which, like other antibiotic resistance (ARE) ABCF proteins, is thought to bind to antibiotic-stalled ribosomes and promote dissociation of the drug from its binding site. To investigate the molecular mechanism by which VmlR confers antibiotic resistance, we have determined a cryo-electron microscopy (cryo-EM) structure of an ATPase-deficient B. subtilis VmlR-EQ2 mutant in complex... (More)

Many Gram-positive pathogenic bacteria employ ribosomal protection proteins (RPPs) to confer resistance to clinically important antibiotics. In Bacillus subtilis, the RPP VmlR confers resistance to lincomycin (Lnc) and the streptogramin A (SA) antibiotic virginiamycin M (VgM). VmlR is an ATP-binding cassette (ABC) protein of the F type, which, like other antibiotic resistance (ARE) ABCF proteins, is thought to bind to antibiotic-stalled ribosomes and promote dissociation of the drug from its binding site. To investigate the molecular mechanism by which VmlR confers antibiotic resistance, we have determined a cryo-electron microscopy (cryo-EM) structure of an ATPase-deficient B. subtilis VmlR-EQ2 mutant in complex with a B. subtilis ErmDL-stalled ribosomal complex (SRC). The structure reveals that VmlR binds within the E site of the ribosome, with the antibiotic resistance domain (ARD) reaching into the peptidyltransferase center (PTC) of the ribosome and a C-terminal extension (CTE) making contact with the small subunit (SSU). To access the PTC, VmlR induces a conformational change in the P-site tRNA, shifting the acceptor arm out of the PTC and relocating the CCA end of the P-site tRNA toward the A site. Together with microbiological analyses, our study indicates that VmlR allosterically dissociates the drug from its ribosomal binding site and exhibits specificity to dislodge VgM, Lnc, and the pleuromutilin tiamulin (Tia), but not chloramphenicol (Cam), linezolid (Lnz), nor the macrolide erythromycin (Ery).

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publishing date
type
Contribution to journal
publication status
published
subject
keywords
ABC ATPase, Antibiotic resistance, Cryo-EM, Ribosome, VmlR
in
Proceedings of the National Academy of Sciences of the United States of America
volume
115
issue
36
pages
6 pages
publisher
National Academy of Sciences
external identifiers
  • scopus:85052758620
  • pmid:30126986
ISSN
0027-8424
DOI
10.1073/pnas.1808535115
language
English
LU publication?
no
additional info
Funding Information: ACKNOWLEDGMENTS. We thank Susanne Rieder for expert technical assistance and Seki Takahiro for generating the ΔvmlR strain. This research was supported by Deutsche Forschungsgemeinschaft Grants FOR1805 and WI3285/8-1 (to D.N.W.), Swedish Research Council Grants 2013-4680 (to V.H.) and 2015-04746 (to G.C.A.), the Ragnar Söderberg Foundation (V.H.), Carl Tryggers stiftelse CTS 34 (G.C.A.), Jeanssons stiftelse (G.C.A.), and from the Umeå Centre for Microbial Research (UCMR): postdoctoral grant 2017 (to H.T.) and Gender Policy Support 2017 (to G.C.A.). iNEXT, project number 5966, was funded by the Horizon 2020 program of the European Union. Czech Infrastructure for Integrative Structural Biology research infrastructure project LM2015043 funded by Ministry of Education, Youth, and Sports of the Czech Republic is gratefully acknowledged for the financial support of the measurements at the CF Cryo-electron Microscopy and Tomography Central European Institute of Technology, Masaryk University. This article reflects only the author’s view, and the European Commission is not responsible for any use that may be made of the information it contains. Publisher Copyright: © 2018 National Academy of Sciences. All Rights Reserved. Copyright: Copyright 2018 Elsevier B.V., All rights reserved.
id
00f6d39a-3a4c-40c7-a41e-ddc2245ed079
date added to LUP
2021-09-24 20:38:05
date last changed
2024-06-16 19:34:44
@article{00f6d39a-3a4c-40c7-a41e-ddc2245ed079,
  abstract     = {{<p>Many Gram-positive pathogenic bacteria employ ribosomal protection proteins (RPPs) to confer resistance to clinically important antibiotics. In Bacillus subtilis, the RPP VmlR confers resistance to lincomycin (Lnc) and the streptogramin A (S<sub>A</sub>) antibiotic virginiamycin M (VgM). VmlR is an ATP-binding cassette (ABC) protein of the F type, which, like other antibiotic resistance (ARE) ABCF proteins, is thought to bind to antibiotic-stalled ribosomes and promote dissociation of the drug from its binding site. To investigate the molecular mechanism by which VmlR confers antibiotic resistance, we have determined a cryo-electron microscopy (cryo-EM) structure of an ATPase-deficient B. subtilis VmlR-EQ<sub>2</sub> mutant in complex with a B. subtilis ErmDL-stalled ribosomal complex (SRC). The structure reveals that VmlR binds within the E site of the ribosome, with the antibiotic resistance domain (ARD) reaching into the peptidyltransferase center (PTC) of the ribosome and a C-terminal extension (CTE) making contact with the small subunit (SSU). To access the PTC, VmlR induces a conformational change in the P-site tRNA, shifting the acceptor arm out of the PTC and relocating the CCA end of the P-site tRNA toward the A site. Together with microbiological analyses, our study indicates that VmlR allosterically dissociates the drug from its ribosomal binding site and exhibits specificity to dislodge VgM, Lnc, and the pleuromutilin tiamulin (Tia), but not chloramphenicol (Cam), linezolid (Lnz), nor the macrolide erythromycin (Ery).</p>}},
  author       = {{Crowe-McAuliffe, Caillan and Graf, Michael and Huter, Paul and Takada, Hiraku and Abdelshahid, Maha and Nováček, Jirí and Murina, Victoriia and Atkinson, Gemma C. and Гaврилюк, Bacилий and Wilson, Daniel N.}},
  issn         = {{0027-8424}},
  keywords     = {{ABC ATPase; Antibiotic resistance; Cryo-EM; Ribosome; VmlR}},
  language     = {{eng}},
  month        = {{09}},
  number       = {{36}},
  pages        = {{8978--8983}},
  publisher    = {{National Academy of Sciences}},
  series       = {{Proceedings of the National Academy of Sciences of the United States of America}},
  title        = {{Structural basis for antibiotic resistance mediated by the Bacillus subtilis ABCF ATPase VmlR}},
  url          = {{http://dx.doi.org/10.1073/pnas.1808535115}},
  doi          = {{10.1073/pnas.1808535115}},
  volume       = {{115}},
  year         = {{2018}},
}