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TitleDirect visualization of ribosomes in the cell-free system revealed the functional evolution of aminoglycoside.
Journal, issue, pagesJ Biochem, Year 2024
Publish dateJan 16, 2024
AuthorsJunta Tomono / Kosuke Asano / Takuma Chiashi / Masato Suzuki / Masayuki Igarashi / Yoshiaki Takahashi / Yoshikazu Tanaka / Takeshi Yokoyama /
PubMed AbstractThe rapid emergence of multi-drug-resistant bacteria has raised a serious public health concern. Therefore, new antibiotic developments have been highly desired. Here, we propose a new method to ...The rapid emergence of multi-drug-resistant bacteria has raised a serious public health concern. Therefore, new antibiotic developments have been highly desired. Here, we propose a new method to visualize antibiotic actions on translating ribosomes in the cell-free system under macromolecular crowding conditions by cryo-electron microscopy, designated as the DARC method: the Direct visualization of Antibiotic binding on Ribosomes in the Cell-free translation system. This new method allows for acquiring a more comprehensive understanding of the mode of action of antibiotics on the translation inhibition without ribosome purification. Furthermore, with the direct link to biochemical analysis at the same condition as cryo-EM observation, we revealed the evolution of 2-DOS aminoglycosides from dibekacin (DBK) to arbekacin (ABK) by acquiring the synthetic tailored anchoring motif to lead to stronger binding affinity to ribosomes. Our cryo-EM structures of DBK and ABK bound ribosomes in the cell-free environment clearly depicted a synthetic tailored γ-amino-α-hydroxybutyryl (HABA) motif formed additional interactions with the ribosome enhancing antibiotic bindings. This new approach would be valuable for understanding the function of antibiotics for more efficient drug development.
External linksJ Biochem / PubMed:38227611
MethodsEM (single particle)
Resolution2.43 - 2.9 Å
Structure data

35411

8ifb

EMDB-35411, PDB-8ifb:
Dibekacin-bound E.coli 70S ribosome in the PURE system
Method: EM (single particle) / Resolution: 2.43 Å

35412

8ifc

EMDB-35412, PDB-8ifc:
Arbekacin-bound E.coli 70S ribosome in the PURE system
Method: EM (single particle) / Resolution: 2.9 Å

35413

8ifd

EMDB-35413, PDB-8ifd:
Dibekacin-added human 80S ribosome
Method: EM (single particle) / Resolution: 2.59 Å

35414

8ife

EMDB-35414, PDB-8ife:
Arbekacin-added human 80S ribosome
Method: EM (single particle) / Resolution: 2.57 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-SPD:
SPERMIDINE / Spermidine

ChemComp-84D:
Dibekacin / antibiotic*YM / Dibekacin

ChemComp-SPM:
SPERMINE / Spermine

ChemComp-ZN:
Unknown entry

ChemComp-84G:
Arbekacin / antibiotic*YM / Arbekacin

Source
  • escherichia coli (E. coli)
  • homo sapiens (human)
KeywordsRIBOSOME

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