Cryo‐EM structure of the ribosome functional complex of the human pathogen <i>Staphylococcus aureus</i> at 3.2 Å resolution

Голубев, А. А.; Fatkhullin, Bulat; Khusainov, Iskander; Jenner, L.; Габдулхаков, А.Г.; Validov, Shamil; Yusupova, G.; Yusupov, Marat; Usachev, Konstantin S.

doi:10.1002/1873-3468.13915

Cited by 21 publications

(21 citation statements)

References 88 publications

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“…We have used our high-resolution maps to present a model of the ribosome from the Gram-positive pathogen L. monocytogenes and update the model of the S. aureus ribosome 57 . Our models of the E. faecalis and S. aureus ribosomes are in good agreement with those recently described 58 , 59 .…”

Section: Resultssupporting

confidence: 90%

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

et al. 2021

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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.

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Section: Resultssupporting

confidence: 90%

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

et al. 2021

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“…Additionally, we have used our high-resolution map to create an updated model of the S. aureus ribosome (Khusainov et al , 2016). Our models of the E. faecalis and S. aureus ribosomes are generally in agreement with those recently described (Golubev et al , 2020; Murphy et al , 2020).…”

Section: Resultssupporting

confidence: 91%

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

Crowe‐McAuliffe

Murina

Turnbull

et al. 2020

Preprint

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Target protection proteins bind to antibiotic targets and confer resistance to the host organism. One class of such proteins, termed antibiotic resistance (ARE) ATP binding cassette (ABC) proteins of the F-subtype (ARE ABCFs), are widely distributed throughout Gram-positive bacteria and bind the ribosome to alleviate translational inhibition by antibiotics that target the large ribosomal subunit. Using single-particle cryo-EM, we have solved the structure 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 comparative approach to understanding how these proteins mediate antibiotic resistance on the ribosome. We present evidence of mechanistically diverse allosteric relays converging on a few peptidyltransferase center (PTC) nucleotides, and propose a general model of antibiotic resistance mediated by these ARE ABCFs.

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“…Phenix.douse was used to place water molecules. A recent structure of the S. aureus ribosome with modified nucleotides (PDB ID 6YEF (Golubev et al, 2020)) was compared to the density to check for RNA modifications, and where the density matched the modification with high confidence, that modification was inserted into the E. faecalis 70S model. For PoxtA, homology models were generated by SWISS-MODEL (Waterhouse et al, 2018) using the crystal structure of EttA (PDB ID 4FIN (Boel et al, 2014)) and the previous cryo-EM structure of LsaA (PDB 7NHK) (Crowe- McAuliffe et al, 2021).…”

Section: Molecular Modellingmentioning

confidence: 99%

Structural basis for PoxtA-mediated resistance to Phenicol and Oxazolidinone antibiotics

Crowe‐McAuliffe

Murina

Kasari

et al. 2021

Preprint

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PoxtA and OptrA are ATP binding cassette (ABC) proteins of the F subtype (ABCF) that confer resistance to oxazolidinone, such as linezolid, and phenicol antibiotics, such as chloramphenicol. PoxtA/OptrA are often encoded on mobile genetic elements, facilitating their rapid spread amongst Gram-positive bacteria. These target protection proteins are thought to confer resistance by binding to the ribosome and dislodging the antibiotics from their binding sites. However, a structural basis for their mechanism of action has been lacking. Here we present cryo-electron microscopy structures of PoxtA in complex with the Enterococcus faecalis 70S ribosome at 2.9-3.1A, as well as the complete E. faecalis 70S ribosome at 2.2-2.5 A. The structures reveal that PoxtA binds within the ribosomal E-site with its antibiotic resistance domain (ARD) extending towards the peptidyltransferase center (PTC) on the large ribosomal subunit. At its closest point, the ARD of PoxtA is still located >15A from the linezolid and chloramphenicol binding sites, suggesting that drug release is elicited indirectly. Instead, we observe that the ARD of PoxtA perturbs the CCA-end of the P-site tRNA causing it to shift by ~4A out of the PTC, which correlates with a register shift of one amino acid for the attached nascent polypeptide chain. Given that linezolid and chloramphenicol are context-specific translation elongation inhibitors, we postulate that PoxtA/OptrA confer resistance to oxazolidinones and phenicols indirectly by perturbing the P-site tRNA and thereby altering the conformation of the attached nascent chain to disrupt the drug binding site.

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Cryo‐EM structure of the ribosome functional complex of the human pathogen Staphylococcus aureus at 3.2 Å resolution

Cited by 21 publications

References 88 publications

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

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

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

Structural basis for PoxtA-mediated resistance to Phenicol and Oxazolidinone antibiotics

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