Ribosome•RelA structures reveal the mechanism of stringent response activation
- University of Massachusetts Medical School, United States
- Mayo Medical School, United States
- Brandeis University, United States
Abstract
Stringent response is a conserved bacterial stress response underlying virulence and antibiotic resistance. RelA/SpoT-homolog proteins synthesize transcriptional modulators (p)ppGpp, allowing bacteria to adapt to stresses. RelA is activated during amino-acid starvation, when cognate deacyl-tRNA binds to the ribosomal A (aminoacyl-tRNA) site. We report four cryo-EM structures of E. coli RelA bound to the 70S ribosome, in the absence and presence of deacyl-tRNA accommodating in the 30S A site. The boomerang-shaped RelA with a wingspan of more than 100 Å wraps around the A/R (30S A-site/RelA-bound) tRNA. The CCA end of the A/R tRNA pins the central TGS domain against the 30S subunit, presenting the (p)ppGpp-synthetase domain near the 30S spur. The ribosome and A/R tRNA are captured in three conformations, revealing hitherto elusive states of tRNA engagement with the ribosomal decoding center. Decoding-center rearrangements are coupled with the step-wise 30S-subunit 'closure', providing insights into the dynamics of high-fidelity tRNA decoding.
Data availability
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Structure of RelA bound to ribosome in absence of A/R tRNA (Structure I)Publicly available at the RCSB Protein Data Bank (accession no: 5KPS).
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Structure of RelA bound to ribosome in presence of A/R tRNA (Structure II)Publicly available at the RCSB Protein Data Bank (accession no: 5KPV).
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Structure of RelA bound to ribosome in presence of A/R tRNA (Structure III)Publicly available at the RCSB Protein Data Bank (accession no: 5KPW).
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Structure of RelA bound to ribosome in presence of A/R tRNA (Structure IV)Publicly available at the RCSB Protein Data Bank (accession no: 5KPX).
Article and author information
Author details
Nikolaus Grigorieff
Andrei A Korostelev
Funding
Howard Hughes Medical Institute
- Nikolaus Grigorieff
National Institutes of Health (RO1 GM106105)
- Andrei A Korostelev
National Institutes of Health (PO1 GM62580)
- Nikolaus Grigorieff
Helen Hay Whitney Foundation
- Anna B Loveland
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Rachel Green, Johns Hopkins School of Medicine, United States
Version history
- Received: April 18, 2016
- Accepted: July 18, 2016
- Accepted Manuscript published: July 19, 2016 (version 1)
- Version of Record published: August 4, 2016 (version 2)
Copyright
© 2016, Loveland 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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Ribosome•RelA structures reveal the mechanism of stringent response activation
eLife 5:e17029.
https://doi.org/10.7554/eLife.17029
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