Structural Basis of Cfr-mediated Antimicrobial Resistance and Mechanisms to Evade It

Overview

Journal Nat Chem Biol

Specialties Biochemistry
Biology
Chemistry

Date 2024 Jan 18

PMID 38238495

Authors

Elena V Aleksandrova

Kelvin J Y Wu

Ben I C Tresco

Egor A Syroegin

Erin E Killeavy

Samson M Balasanyants

Maxim S Svetlov

Steven T Gregory

Gemma C Atkinson

Andrew G Myers

Yury S Polikanov

Affiliations

Soon will be listed here.

Abstract

The bacterial ribosome is an essential drug target as many clinically important antibiotics bind and inhibit its functional centers. The catalytic peptidyl transferase center (PTC) is targeted by the broadest array of inhibitors belonging to several chemical classes. One of the most abundant and clinically prevalent resistance mechanisms to PTC-acting drugs in Gram-positive bacteria is C8-methylation of the universally conserved A2503 nucleobase by Cfr methylase in 23S ribosomal RNA. Despite its clinical importance, a sufficient understanding of the molecular mechanisms underlying Cfr-mediated resistance is currently lacking. Here, we report a set of high-resolution structures of the Cfr-modified 70S ribosome containing aminoacyl- and peptidyl-transfer RNAs. These structures reveal an allosteric rearrangement of nucleotide A2062 upon Cfr-mediated methylation of A2503 that likely contributes to the reduced potency of some PTC inhibitors. Additionally, we provide the structural bases behind two distinct mechanisms of engaging the Cfr-methylated ribosome by the antibiotics iboxamycin and tylosin.

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References

Bollenbach T, Quan S, Chait R, Kishony R . Nonoptimal microbial response to antibiotics underlies suppressive drug interactions. Cell. 2009; 139(4):707-18. PMC: 2838386. DOI: 10.1016/j.cell.2009.10.025. View

Toh S, Xiong L, Arias C, Villegas M, Lolans K, Quinn J . Acquisition of a natural resistance gene renders a clinical strain of methicillin-resistant Staphylococcus aureus resistant to the synthetic antibiotic linezolid. Mol Microbiol. 2007; 64(6):1506-14. PMC: 2711439. DOI: 10.1111/j.1365-2958.2007.05744.x. View

Syroegin E, Aleksandrova E, Polikanov Y . Insights into the ribosome function from the structures of non-arrested ribosome-nascent chain complexes. Nat Chem. 2022; 15(1):143-153. PMC: 9840698. DOI: 10.1038/s41557-022-01073-1. View

Goethe O, DiBello M, Herzon S . Total synthesis of structurally diverse pleuromutilin antibiotics. Nat Chem. 2022; 14(11):1270-1277. PMC: 9633427. DOI: 10.1038/s41557-022-01027-7. View

Hansen J, Ippolito J, Ban N, Nissen P, Moore P, Steitz T . The structures of four macrolide antibiotics bound to the large ribosomal subunit. Mol Cell. 2002; 10(1):117-28. DOI: 10.1016/s1097-2765(02)00570-1. View

Polikanov Y, Starosta A, Juette M, Altman R, Terry D, Lu W . Distinct tRNA Accommodation Intermediates Observed on the Ribosome with the Antibiotics Hygromycin A and A201A. Mol Cell. 2015; 58(5):832-44. PMC: 4458074. DOI: 10.1016/j.molcel.2015.04.014. View

Dunkle J, Xiong L, Mankin A, Cate J . Structures of the Escherichia coli ribosome with antibiotics bound near the peptidyl transferase center explain spectra of drug action. Proc Natl Acad Sci U S A. 2010; 107(40):17152-7. PMC: 2951456. DOI: 10.1073/pnas.1007988107. View

Shen J, Wang Y, Schwarz S . Presence and dissemination of the multiresistance gene cfr in Gram-positive and Gram-negative bacteria. J Antimicrob Chemother. 2013; 68(8):1697-706. DOI: 10.1093/jac/dkt092. View

McArthur A, Waglechner N, Nizam F, Yan A, Azad M, Baylay A . The comprehensive antibiotic resistance database. Antimicrob Agents Chemother. 2013; 57(7):3348-57. PMC: 3697360. DOI: 10.1128/AAC.00419-13. View

10.

Syroegin E, Flemmich L, Klepacki D, Vazquez-Laslop N, Micura R, Polikanov Y . Structural basis for the context-specific action of the classic peptidyl transferase inhibitor chloramphenicol. Nat Struct Mol Biol. 2022; 29(2):152-161. PMC: 9071271. DOI: 10.1038/s41594-022-00720-y. View

11.

Svetlov M, Plessa E, Chen C, Bougas A, Krokidis M, Dinos G . High-resolution crystal structures of ribosome-bound chloramphenicol and erythromycin provide the ultimate basis for their competition. RNA. 2019; 25(5):600-606. PMC: 6467010. DOI: 10.1261/rna.069260.118. View

12.

Kannan K, Vazquez-Laslop N, Mankin A . Selective protein synthesis by ribosomes with a drug-obstructed exit tunnel. Cell. 2012; 151(3):508-20. DOI: 10.1016/j.cell.2012.09.018. View

13.

Giessing A, Jensen S, Rasmussen A, Hansen L, Gondela A, Long K . Identification of 8-methyladenosine as the modification catalyzed by the radical SAM methyltransferase Cfr that confers antibiotic resistance in bacteria. RNA. 2009; 15(2):327-36. PMC: 2648713. DOI: 10.1261/rna.1371409. View

14.

Madhaiyan M, Wirth J, Saravanan V . Phylogenomic analyses of the family suggest the reclassification of five species within the genus as heterotypic synonyms, the promotion of five subspecies to novel species, the taxonomic reassignment of five species to gen. nov., and the formal.... Int J Syst Evol Microbiol. 2020; 70(11):5926-5936. DOI: 10.1099/ijsem.0.004498. View

15.

Toh S, Xiong L, Bae T, Mankin A . The methyltransferase YfgB/RlmN is responsible for modification of adenosine 2503 in 23S rRNA. RNA. 2007; 14(1):98-106. PMC: 2151032. DOI: 10.1261/rna.814408. View

16.

Osterman I, Khabibullina N, Komarova E, Kasatsky P, Kartsev V, Bogdanov A . Madumycin II inhibits peptide bond formation by forcing the peptidyl transferase center into an inactive state. Nucleic Acids Res. 2017; 45(12):7507-7514. PMC: 5499580. DOI: 10.1093/nar/gkx413. View

17.

Pfister P, Jenni S, Poehlsgaard J, Thomas A, Douthwaite S, Ban N . The structural basis of macrolide-ribosome binding assessed using mutagenesis of 23S rRNA positions 2058 and 2059. J Mol Biol. 2004; 342(5):1569-81. DOI: 10.1016/j.jmb.2004.07.095. View

18.

Vazquez-Laslop N, Ramu H, Klepacki D, Kannan K, Mankin A . The key function of a conserved and modified rRNA residue in the ribosomal response to the nascent peptide. EMBO J. 2010; 29(18):3108-17. PMC: 2944061. DOI: 10.1038/emboj.2010.180. View

19.

. UniProt: the Universal Protein Knowledgebase in 2023. Nucleic Acids Res. 2022; 51(D1):D523-D531. PMC: 9825514. DOI: 10.1093/nar/gkac1052. View

20.

Katoh K, Standley D . MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013; 30(4):772-80. PMC: 3603318. DOI: 10.1093/molbev/mst010. View