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

J 2018

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

CROWE-MCAULIFFE, C., M. GRAF, P. HUTER, H. TAKADA, M. ABDELSHAHID et. al.

Basic information

Original name

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

Authors

CROWE-MCAULIFFE, C. (276 Germany), M. GRAF (276 Germany), P. HUTER (276 Germany), H. TAKADA (752 Sweden), M. ABDELSHAHID (276 Germany), Jiří NOVÁČEK (203 Czech Republic, guarantor, belonging to the institution), V. MURINA (752 Sweden), G.C. ATKINSON (752 Sweden), V. HAURYLIUK (752 Sweden) and D.N. WILSON (276 Germany)

Edition

Proceedings of the National Academy of Sciences of the United States of America, WASHINGTON, NATL ACAD SCIENCES, 2018, 0027-8424

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10608 Biochemistry and molecular biology

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

Impact factor

Impact factor: 9.580

RIV identification code

RIV/00216224:14740/18:00106666

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1073/pnas.1808535115

UT WoS

000443555000057

Keywords in English

ABC ATPase; cryo-EM; ribosome; antibiotic resistance; VmlR

Abstract

V originále

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-EQ(2) 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).

Links

LM2015043, research and development project

Name: Česká infrastruktura pro integrativní strukturní biologii (Acronym: CIISB)

Investor: Ministry of Education, Youth and Sports of the CR

Citovat

CROWE-MCAULIFFE, C., M. GRAF, P. HUTER, H. TAKADA, M. ABDELSHAHID, Jiří NOVÁČEK, V. MURINA, G.C. ATKINSON, V. HAURYLIUK and D.N. WILSON. Structural basis for antibiotic resistance mediated by the Bacillus subtilis ABCF ATPase VmlR. Proceedings of the National Academy of Sciences of the United States of America. WASHINGTON: NATL ACAD SCIENCES, 2018, vol. 115, No 36, p. 8978-8983. ISSN 0027-8424. Available from: https://dx.doi.org/10.1073/pnas.1808535115.

@article{1507917,
   author = {CroweandMcAuliffe, C. and Graf, M. and Huter, P. and Takada, H. and Abdelshahid, M. and Nováček, Jiří and Murina, V. and Atkinson, G.C. and Hauryliuk, V. and Wilson, D.N.},
   article_location = {WASHINGTON},
   article_number = {36},
   doi = {http://dx.doi.org/10.1073/pnas.1808535115},
   keywords = {ABC ATPase; cryo-EM; ribosome; antibiotic resistance; VmlR},
   language = {eng},
   issn = {0027-8424},
   journal = {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},
   volume = {115},
   year = {2018}
}

TY  - JOUR
ID  - 1507917
AU  - Crowe-McAuliffe, C. - Graf, M. - Huter, P. - Takada, H. - Abdelshahid, M. - Nováček, Jiří - Murina, V. - Atkinson, G.C. - Hauryliuk, V. - Wilson, D.N.
PY  - 2018
TI  - Structural basis for antibiotic resistance mediated by the Bacillus subtilis ABCF ATPase VmlR
JF  - Proceedings of the National Academy of Sciences of the United States of America
VL  - 115
IS  - 36
SP  - 8978-8983
EP  - 8978-8983
PB  - NATL ACAD SCIENCES
SN  - 00278424
KW  - ABC ATPase
KW  - cryo-EM
KW  - ribosome
KW  - antibiotic resistance
KW  - VmlR
N2  - 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-EQ(2) 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).
ER  -

CROWE-MCAULIFFE, C., M. GRAF, P. HUTER, H. TAKADA, M. ABDELSHAHID, Jiří NOVÁČEK, V. MURINA, G.C. ATKINSON, V. HAURYLIUK and D.N. WILSON. Structural basis for antibiotic resistance mediated by the Bacillus subtilis ABCF ATPase VmlR. \textit{Proceedings of the National Academy of Sciences of the United States of America}. WASHINGTON: NATL ACAD SCIENCES, 2018, vol.~115, No~36, p.~8978-8983. ISSN~0027-8424. Available from: https://dx.doi.org/10.1073/pnas.1808535115.

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