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Aleksandrova EV, Wu KJY, Tresco BIC, Syroegin EA, Killeavy EE, Balasanyants SM, Svetlov MS, Gregory ST, Atkinson GC, Myers AG, Polikanov YS. Structural basis of Cfr-mediated antimicrobial resistance and mechanisms to evade it. Nat Chem Biol 2024:10.1038/s41589-023-01525-w. [PMID: 38238495 DOI: 10.1038/s41589-023-01525-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 12/11/2023] [Indexed: 01/30/2024]
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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Affiliation(s)
- Elena V Aleksandrova
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Kelvin J Y Wu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Ben I C Tresco
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Egor A Syroegin
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Erin E Killeavy
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, RI, USA
| | - Samson M Balasanyants
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Maxim S Svetlov
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Steven T Gregory
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, RI, USA
| | - Gemma C Atkinson
- Department of Experimental Medicine, Lund University, Lund, Sweden
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Andrew G Myers
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
| | - Yury S Polikanov
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, USA.
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA.
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA.
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Aleksandrova EV, Wu KJY, Tresco BIC, Syroegin EA, Killeavy EE, Balasanyants SM, Svetlov MS, Gregory ST, Atkinson GC, Myers AG, Polikanov YS. Structural basis of Cfr-mediated antimicrobial resistance and mechanisms for its evasion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.27.559749. [PMID: 37808676 PMCID: PMC10557674 DOI: 10.1101/2023.09.27.559749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
The ribosome is an essential drug target as many classes of 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 mechanisms of resistance to PTC-acting drugs is C8-methylation of the universally conserved adenine residue 2503 (A2503) of the 23S rRNA by the methyltransferase Cfr. Despite its clinical significance, a sufficient understanding of the molecular mechanisms underlying Cfr-mediated resistance is currently lacking. In this work, we developed a method to express a functionally-active Cfr-methyltransferase in the thermophilic bacterium Thermus thermophilus and report a set of high-resolution structures of the Cfr-modified 70S ribosome containing aminoacyl- and peptidyl-tRNAs. Our structures reveal that an allosteric rearrangement of nucleotide A2062 upon Cfr-methylation of A2503 is likely responsible for the inability of some PTC inhibitors to bind to the ribosome, providing additional insights into the Cfr resistance mechanism. Lastly, by determining the structures of the Cfr-methylated ribosome in complex with the antibiotics iboxamycin and tylosin, we provide the structural bases behind two distinct mechanisms of evading Cfr-mediated resistance.
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Affiliation(s)
- Elena V. Aleksandrova
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Kelvin J. Y. Wu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Ben I. C. Tresco
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Egor A. Syroegin
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Erin E. Killeavy
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, RI 02881, USA
| | - Samson M. Balasanyants
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Maxim S. Svetlov
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Steven T. Gregory
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, RI 02881, USA
| | - Gemma C. Atkinson
- Department of Experimental Medicine, University of Lund, Lund, Sweden
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
| | - Andrew G. Myers
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Yury S. Polikanov
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
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Obana N, Takada H, Crowe-McAuliffe C, Iwamoto M, Egorov AA, Wu KJY, Chiba S, Murina V, Paternoga H, Tresco BIC, Nomura N, Myers AG, Atkinson G, Wilson DN, Hauryliuk V. Genome-encoded ABCF factors implicated in intrinsic antibiotic resistance in Gram-positive bacteria: VmlR2, Ard1 and CplR. Nucleic Acids Res 2023; 51:4536-4554. [PMID: 36951104 PMCID: PMC10201436 DOI: 10.1093/nar/gkad193] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/17/2023] [Accepted: 03/06/2023] [Indexed: 03/24/2023] Open
Abstract
Genome-encoded antibiotic resistance (ARE) ATP-binding cassette (ABC) proteins of the F subfamily (ARE-ABCFs) mediate intrinsic resistance in diverse Gram-positive bacteria. The diversity of chromosomally-encoded ARE-ABCFs is far from being fully experimentally explored. Here we characterise phylogenetically diverse genome-encoded ABCFs from Actinomycetia (Ard1 from Streptomyces capreolus, producer of the nucleoside antibiotic A201A), Bacilli (VmlR2 from soil bacterium Neobacillus vireti) and Clostridia (CplR from Clostridium perfringens, Clostridium sporogenes and Clostridioides difficile). We demonstrate that Ard1 is a narrow spectrum ARE-ABCF that specifically mediates self-resistance against nucleoside antibiotics. The single-particle cryo-EM structure of a VmlR2-ribosome complex allows us to rationalise the resistance spectrum of this ARE-ABCF that is equipped with an unusually long antibiotic resistance determinant (ARD) subdomain. We show that CplR contributes to intrinsic pleuromutilin, lincosamide and streptogramin A resistance in Clostridioides, and demonstrate that C. difficile CplR (CDIF630_02847) synergises with the transposon-encoded 23S ribosomal RNA methyltransferase Erm to grant high levels of antibiotic resistance to the C. difficile 630 clinical isolate. Finally, assisted by uORF4u, our novel tool for detection of upstream open reading frames, we dissect the translational attenuation mechanism that controls the induction of cplR expression upon an antibiotic challenge.
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Affiliation(s)
- Nozomu Obana
- Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
- Microbiology Research Center for Sustainability (MiCS), University of Tsukuba, Tsukuba, Japan
| | - Hiraku Takada
- Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku, Kyoto 603-8555, Japan
- Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Caillan Crowe-McAuliffe
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Mizuki Iwamoto
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Artyom A Egorov
- Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Kelvin J Y Wu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Shinobu Chiba
- Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku, Kyoto 603-8555, Japan
- Institute for Protein Dynamics, Kyoto Sangyo University, Japan
| | | | - Helge Paternoga
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Ben I C Tresco
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Nobuhiko Nomura
- Microbiology Research Center for Sustainability (MiCS), University of Tsukuba, Tsukuba, Japan
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Andrew G Myers
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Gemma C Atkinson
- Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Daniel N Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Vasili Hauryliuk
- Department of Experimental Medical Science, Lund University, Lund, Sweden
- University of Tartu, Institute of Technology, Tartu, Estonia
- Science for Life Laboratory, Lund, Sweden
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Koller TO, Turnbull KJ, Vaitkevicius K, Crowe-McAuliffe C, Roghanian M, Bulvas O, Nakamoto JA, Kurata T, Julius C, Atkinson G, Johansson J, Hauryliuk V, Wilson D. Structural basis for HflXr-mediated antibiotic resistance in Listeria monocytogenes. Nucleic Acids Res 2022; 50:11285-11300. [PMID: 36300626 PMCID: PMC9638945 DOI: 10.1093/nar/gkac934] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 09/28/2022] [Accepted: 10/26/2022] [Indexed: 08/09/2023] Open
Abstract
HflX is a ubiquitous bacterial GTPase that splits and recycles stressed ribosomes. In addition to HflX, Listeria monocytogenes contains a second HflX homolog, HflXr. Unlike HflX, HflXr confers resistance to macrolide and lincosamide antibiotics by an experimentally unexplored mechanism. Here, we have determined cryo-EM structures of L. monocytogenes HflXr-50S and HflX-50S complexes as well as L. monocytogenes 70S ribosomes in the presence and absence of the lincosamide lincomycin. While the overall geometry of HflXr on the 50S subunit is similar to that of HflX, a loop within the N-terminal domain of HflXr, which is two amino acids longer than in HflX, reaches deeper into the peptidyltransferase center. Moreover, unlike HflX, the binding of HflXr induces conformational changes within adjacent rRNA nucleotides that would be incompatible with drug binding. These findings suggest that HflXr confers resistance using an allosteric ribosome protection mechanism, rather than by simply splitting and recycling antibiotic-stalled ribosomes.
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Affiliation(s)
| | | | - Karolis Vaitkevicius
- Department of Molecular Biology and Umeå Centre for Microbial Research (UCMR), Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90187 Umeå, Sweden
| | - Caillan Crowe-McAuliffe
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Mohammad Roghanian
- Department of Molecular Biology and Umeå Centre for Microbial Research (UCMR), Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90187 Umeå, Sweden
- Department of Clinical Microbiology, Rigshospitalet, 2200 Copenhagen, Denmark
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
| | - Ondřej Bulvas
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technicka 5, 166 28 Prague 6, Czech Republic
| | - Jose A Nakamoto
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
| | - Tatsuaki Kurata
- Department of Molecular Biology and Umeå Centre for Microbial Research (UCMR), Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90187 Umeå, Sweden
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
| | - Christina Julius
- Department of Molecular Biology and Umeå Centre for Microbial Research (UCMR), Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90187 Umeå, Sweden
| | - Gemma C Atkinson
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
| | - Jörgen Johansson
- Department of Molecular Biology and Umeå Centre for Microbial Research (UCMR), Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90187 Umeå, Sweden
| | | | - Daniel N Wilson
- To whom correspondence should be addressed. Tel: +49 40 42838 2841;
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