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The antibiotic kasugamycin mimics mRNA nucleotides to destabilize tRNA binding and inhibit canonical translation initiation

Nature Structural & Molecular Biology volume 13, pages 871–878 (2006)Cite this article

An Erratum to this article was published on 01 November 2006

This article has been updated

Abstract

Kasugamycin (Ksg) specifically inhibits translation initiation of canonical but not of leaderless messenger RNAs. Ksg inhibition is thought to occur by direct competition with initiator transfer RNA. The 3.35-Å structure of Ksg bound to the 30S ribosomal subunit presented here provides a structural description of two Ksg-binding sites as well as a basis for understanding Ksg resistance. Notably, neither binding position overlaps with P-site tRNA; instead, Ksg mimics codon nucleotides at the P and E sites by binding within the path of the mRNA. Coupled with biochemical experiments, our results suggest that Ksg indirectly inhibits P-site tRNA binding through perturbation of the mRNA-tRNA codon-anticodon interaction during 30S canonical initiation. In contrast, for 70S-type initiation on leaderless mRNA, the overlap between mRNA and Ksg is reduced and the binding of tRNA is further stabilized by the presence of the 50S subunit, minimizing Ksg efficacy.

*NOTE: In the version of this article initially published, the author name Mikako Shirouzo was spelled incorrectly. The correct author name is Mikako Shirouzu. This error has been corrected in the HTML and PDF versions of the article.

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Figure 1: The primary and secondary Ksg-binding sites on the T. thermophilus 30S subunit.
Figure 2: Interaction of Ksg with the 30S subunit.
Figure 3: Ksg overlaps with P-site mRNA but not P-tRNA.
Figure 4: Inhibition of P-site tRNA binding by Ksg.
Figure 5: Lack of methylation of A1518 and A1519 confers Ksg resistance indirectly.
Figure 6: Model for Ksg action during translation initiation.

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Acknowledgements

We would like to thank R. Albrecht, J. Buerger, B. Schmidt and M. Nomura for technical assistance and S. Connell for helpful discussions. These studies could not have been performed without the expert assistance of the staff, especially T. Tomizaki and C. Schulze-Briese, at the X06SA beamline (Swiss Light Source). This work was funded by the RIKEN Structural Genomics/Proteomics Initiative and the National Project on Protein Structural and Functional Analyses, Ministry of Education, Culture, Sports, Science and Technology of Japan (S.Y.) and by the Deutsche Forschungs Gemeinschaft (FU579 to P.F.).

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Author notes

  1. Frank Schluenzen, Chie Takemoto, Daniel N Wilson and Tatsuya Kaminishi: These authors contributed equally to this work.

Authors and Affiliations

  1. Max-Planck Institute for Molecular Genetics, Berlin, D-14195, Germany

    Frank Schluenzen, Daniel N Wilson, Joerg M Harms, Witold Szaflarski, Knud H Nierhaus & Paola Fucini

  2. RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, 230-0045, Yokohama, Japan

    Chie Takemoto, Tatsuya Kaminishi, Kyoko Hanawa-Suetsugu, Masahito Kawazoe, Mikako Shirouzu & Shigeyuki Yokoyama

  3. Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, 113-0033, Tokyo, Japan

    Shigeyuki Yokoyama

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  1. Frank Schluenzen
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Supplementary information

Supplementary Fig. 1

Stereo image of density for Ksg bound within the primary and secondary sites. (PDF 202 kb)

Supplementary Fig. 2

Phylogenetic conservation of 16S rRNA and comparison of Ksg2 binding site on 30S and 70S ribosomes. (PDF 150 kb)

Supplementary Fig. 3

Position of Ksg relative to Spur-ASL, tRNA and mRNA. (PDF 134 kb)

Supplementary Table 1

Data collection and refinement statistics. (PDF 38 kb)

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Schluenzen, F., Takemoto, C., Wilson, D. et al. The antibiotic kasugamycin mimics mRNA nucleotides to destabilize tRNA binding and inhibit canonical translation initiation. Nat Struct Mol Biol 13, 871–878 (2006). https://doi.org/10.1038/nsmb1145

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