The mechanism of error induction by the antibiotic viomycin provides insight into the fidelity mechanism of translation

Abstract

Applying pre-steady state kinetics to an Escherichia coli based reconstituted translation system we have studied how the antibiotic viomycin affects the accuracy of genetic code reading. We find that viomycin binds to translating ribosomes associated with a ternary complex (TC) consisting of elongation factor Tu (EF-Tu), aminoacyl tRNA and GTP, and locks the otherwise dynamically flipping monitoring bases A1492 and A1493 into their active conformation. This effectively prevents dissociation of near- and non-cognate TCs from the ribosome, thereby enhancing errors in initial selection. Moreover, viomycin shuts down proofreading based error correction. Our results imply a mechanism in which the accuracy of initial selection is achieved by larger backward rate constants towards TC dissociation rather than by a smaller rate constant for GTP hydrolysis for near- and non-cognate TCs. Additionally, our results demonstrate that translocation inhibition, rather than error induction, is the major cause of cell growth inhibition by viomycin.

Data availability

All data generated or analysed during this study are included in the manuscript.

Article and author information

Author details

  1. Mikael Holm

    Department of Cell and Molecular biology, Uppsala University, Uppsala, Sweden
    Competing interests
    The authors declare that no competing interests exist.
  2. Chandra Sekhar Mandava

    Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
    Competing interests
    The authors declare that no competing interests exist.
  3. Måns Ehrenberg

    Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
    Competing interests
    The authors declare that no competing interests exist.
  4. Suparna Sanyal

    Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
    For correspondence
    suparna.sanyal@icm.uu.se
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7124-792X

Funding

Swedish Research Council (2018-05498 (NT))

  • Suparna Sanyal

Carl Tryggers Stiftelse för Vetenskaplig Forskning (CTS 18: 338)

  • Suparna Sanyal

Wenner-Gren Foundation (UPD2017-0238)

  • Suparna Sanyal

Knut och Alice Wallenbergs Stiftelse (KAW 2011.0081 to RiboCORE)

  • Suparna Sanyal

Knut och Alice Wallenbergs Stiftelse (KAW 2017.0055)

  • Suparna Sanyal

Swedish Research Council (2016-06264 (Research Environment))

  • Suparna Sanyal

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Alan G Hinnebusch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, United States

Version history

  1. Received: March 4, 2019
  2. Accepted: June 4, 2019
  3. Accepted Manuscript published: June 7, 2019 (version 1)
  4. Version of Record published: June 26, 2019 (version 2)

Copyright

© 2019, Holm et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Mikael Holm
  2. Chandra Sekhar Mandava
  3. Måns Ehrenberg
  4. Suparna Sanyal
(2019)
The mechanism of error induction by the antibiotic viomycin provides insight into the fidelity mechanism of translation
eLife 8:e46124.
https://doi.org/10.7554/eLife.46124

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https://doi.org/10.7554/eLife.46124

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