TY - JOUR
T1 - Structures of the Staphylococcus aureus ribosome inhibited by fusidic acid and fusidic acid cyclopentane
AU - González-López, Adrián
AU - Larsson, Daniel S.D.
AU - Koripella, Ravi Kiran
AU - Cain, Brett N.
AU - Chavez, Martin Garcia
AU - Hergenrother, Paul J.
AU - Sanyal, Suparna
AU - Selmer, Maria
N1 - We thank Diarmaid Hughes for providing the S. aureus strain, Michael Hall for assistance with cryo-EM data collection, and Filipe Maia for maintaining our local computer cluster. We acknowledge the use of the Cryo-EM Uppsala facility for grid preparation and screening, funded by the Department of Cell and Molecular Biology, the Disciplinary Domains of Science and Technology and of Medicine and Pharmacy at Uppsala University. Cryo-EM data were collected at the Cryo-EM Swedish National Facility funded by the Knut and Alice Wallenberg Foundation, the Erling-Persson Family Foundation, and the Kempe Foundation; SciLifeLab; Stockholm University; and Ume\u00E5 University. This research was funded by grants from Uppsala Antibiotic Center to M.S., from the Swedish Research Council (2017-03827 and 2022-04511 to M.S.; 2023-05237,\u00A02018-05946 and 2018-05498 to S.S.; 2016-06264 to M.S. and S.S.) and from the Knut and Alice Wallenberg Foundation (KAW 2017.0055) to S.S. A.G.L. has received a fellowship from the Sven and Lilly Lawski Foundation.\u00A0P.J.H. thanks NIH-NIAID (AI136773) for funding.\u00A0M.G.C. was a member of the NIH Chemistry-Biology Interface Training Grant, T32-GM136629.
We thank Diarmaid Hughes for providing the S. aureus strain, Michael Hall for assistance with cryo-EM data collection, and Filipe Maia for maintaining our local computer cluster. We acknowledge the use of the Cryo-EM Uppsala facility for grid preparation and screening, funded by the Department of Cell and Molecular Biology, the Disciplinary Domains of Science and Technology and of Medicine and Pharmacy at Uppsala University. Cryo-EM data were collected at the Cryo-EM Swedish National Facility funded by the Knut and Alice Wallenberg Foundation, the Erling-Persson Family Foundation, and the Kempe Foundation; SciLifeLab; Stockholm University; and Ume\u00E5 University. This research was funded by grants from Uppsala Antibiotic Center to M.S., from the Swedish Research Council (2017-03827 and 2022-04511 to M.S.; 2023-05237, 2018-05946 and 2018-05498 to S.S.; 2016-06264 to M.S. and S.S.) and from the Knut and Alice Wallenberg Foundation (KAW 2017.0055) to S.S. A.G.L. has received a fellowship from the Sven and Lilly Lawski Foundation. P.J.H. thanks NIH-NIAID (AI136773) for funding. M.G.C. was a member of the NIH Chemistry-Biology Interface Training Grant, T32-GM136629.
PY - 2024/12
Y1 - 2024/12
N2 - The antibiotic fusidic acid (FA) is used to treat Staphylococcus aureus infections. It inhibits protein synthesis by binding to elongation factor G (EF-G) and preventing its release from the ribosome after translocation. While FA, due to permeability issues, is only effective against gram-positive bacteria, the available structures of FA-inhibited complexes are from gram-negative model organisms. To fill this knowledge gap, we solved cryo-EM structures of the S. aureus ribosome in complex with mRNA, tRNA, EF-G and FA to 2.5 Å resolution and the corresponding complex structures with the recently developed FA derivative FA-cyclopentane (FA-CP) to 2.0 Å resolution. With both FA variants, the majority of the ribosomal particles are observed in chimeric state and only a minor population in post-translocational state. As expected, FA binds in a pocket between domains I, II and III of EF-G and the sarcin-ricin loop of 23S rRNA. FA-CP binds in an identical position, but its cyclopentane moiety provides additional contacts to EF-G and 23S rRNA, suggesting that its improved resistance profile towards mutations in EF-G is due to higher-affinity binding. These high-resolution structures reveal new details about the S. aureus ribosome, including confirmation of many rRNA modifications, and provide an optimal starting point for future structure-based drug discovery on an important clinical drug target.
AB - The antibiotic fusidic acid (FA) is used to treat Staphylococcus aureus infections. It inhibits protein synthesis by binding to elongation factor G (EF-G) and preventing its release from the ribosome after translocation. While FA, due to permeability issues, is only effective against gram-positive bacteria, the available structures of FA-inhibited complexes are from gram-negative model organisms. To fill this knowledge gap, we solved cryo-EM structures of the S. aureus ribosome in complex with mRNA, tRNA, EF-G and FA to 2.5 Å resolution and the corresponding complex structures with the recently developed FA derivative FA-cyclopentane (FA-CP) to 2.0 Å resolution. With both FA variants, the majority of the ribosomal particles are observed in chimeric state and only a minor population in post-translocational state. As expected, FA binds in a pocket between domains I, II and III of EF-G and the sarcin-ricin loop of 23S rRNA. FA-CP binds in an identical position, but its cyclopentane moiety provides additional contacts to EF-G and 23S rRNA, suggesting that its improved resistance profile towards mutations in EF-G is due to higher-affinity binding. These high-resolution structures reveal new details about the S. aureus ribosome, including confirmation of many rRNA modifications, and provide an optimal starting point for future structure-based drug discovery on an important clinical drug target.
KW - Cryo-EM
KW - EF-G
KW - Elongation factor G
KW - Fusidic acid
KW - Ribosome
UR - http://www.scopus.com/inward/record.url?scp=85196551467&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85196551467&partnerID=8YFLogxK
U2 - 10.1038/s41598-024-64868-x
DO - 10.1038/s41598-024-64868-x
M3 - Article
C2 - 38902339
AN - SCOPUS:85196551467
SN - 2045-2322
VL - 14
JO - Scientific reports
JF - Scientific reports
IS - 1
M1 - 14253
ER -