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Structure-function insights into higher potency of antibiotic arbekacin in inhibiting bacterial protein synthesis
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.ORCID iD: 0000-0002-3228-9908
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
(English)Manuscript (preprint) (Other academic)
Keywords [en]
Aminglycosides, Arbekacin, AHB moiety, Ribosome, Dwelling-time, Translation
National Category
Biochemistry Molecular Biology
Research subject
Biology with specialization in Molecular Biology; Biochemistry; Biology with specialization in Structural Biology
Identifiers
URN: urn:nbn:se:uu:diva-486745OAI: oai:DiVA.org:uu-486745DiVA, id: diva2:1704845
Available from: 2022-10-19 Created: 2022-10-19 Last updated: 2025-02-20
In thesis
1. Molecular Interplay of Antibiotics on the Bacterial Ribosome
Open this publication in new window or tab >>Molecular Interplay of Antibiotics on the Bacterial Ribosome
2022 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Inhibition of protein synthesis is one of the most common modes of action for medically useful antibiotics. This thesis presents the mechanistic studies of two chemically distinct classes of antibiotics that target bacterial ribosomes –aminoglycosides and thermorubin. Arbekacin (ABK) and amikacin (AMK) are two new-generation semisynthetic aminoglycosides (AGAs) that were developed to overcome enzyme-mediated AGA resistance in bacteria. Our results demonstrate that these two antibiotics induce potent inhibitory effects on various phases of bacterial protein synthesis. The binding of ABK stalls elongating ribosomes to a state that is unfavorable for elongation factor-G (EF-G) binding, which drastically prolongs the time for translocation from ~50 milliseconds to at least 2 seconds. ABK also abolishes the accuracy of mRNA decoding and inhibits peptide release. The results of in vitro fast kinetics and structures of ABK and AMK-bound 70S ribosomes reveal that in addition to canonical binding at h44 of 16S rRNA, appended amino-hydroxy butyryl (AHB) moiety of ABK and AMK secures extra interactions at the binding pocket and provides long dwelling-time on the translating ribosome. Moreover, AMK binds at the large subunit of ribosome proximal to the 3'CCA-end of the tRNA in the P-site and inhibits the release factor-mediated peptide release. Our data suggest that AGA impose bacteriostatic effects mainly by inhibiting translocation, while they become bactericidal in combination with decoding errors. We have further characterized the molecular mechanism of action of the antibiotic thermorubin (THB) using in vitro fast kinetics and cryo-EM. We found that THB impedes elongation, termination, and ribosome recycling phases of translation. THB does so by binding to the intersubunit bridge B2a and extruding C1914 of H69 of 23S rRNA that interferes with the interactions of A-site substrates including aminoacyl-tRNAs, class-I release factors, and ribosome recycling factor. We also found that THB acts as an anti-dissociation agent that tethers the ribosomal subunits and blocks ribosome recycling, subsequently reducing the pool of active ribosomes. These studies altogether suggest that in-depth characterization of antibiotic action provides important clues that hopefully aid in the development of new antibiotics to fight against looming antibiotic resistance.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2022. p. 62
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 2205
Keywords
Ribosome, Translation, Antibiotics, Aminoglycoside, Thermorubin, Protein synthesis
National Category
Biochemistry Molecular Biology Structural Biology
Research subject
Molecular Life Sciences
Identifiers
urn:nbn:se:uu:diva-486907 (URN)978-91-513-1635-2 (ISBN)
Public defence
2022-12-09, BMC, A1:107a, Husargatan 3, Uppsala, 09:15 (English)
Opponent
Supervisors
Note

Date of Defence: Friday 9 December 2022 (9:15 am)

Available from: 2022-11-16 Created: 2022-10-20 Last updated: 2025-02-20

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CiteExportLink to record
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Citation style
  • apa
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