Ribosome•RelA structures reveal the mechanism of stringent response activation

Abstract
Data availability
Article and author information
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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

The following data sets were generated

1. Loveland AB
2. Bah E
3. Madireddy R
4. Zhang Y
5. Brilot AF
6. Grigorieff N
7. Korostelev AA
(2016) 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).

http://www.rcsb.org/pdb/explore/explore.do?structureId=5KPS
1. Loveland AB
2. Bah E
3. Madireddy R
4. Zhang Y
5. Brilot AF
6. Grigorieff N
7. Korostelev AA
(2016) 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).

http://www.rcsb.org/pdb/explore/explore.do?structureId=5KPV
1. Loveland AB
2. Bah E
3. Madireddy R
4. Zhang Y
5. Brilot AF
6. Grigorieff N
7. Korostelev AA
(2016) 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).

http://www.rcsb.org/pdb/explore/explore.do?structureId=5KPW
1. Loveland AB
2. Bah E
3. Madireddy R
4. Zhang Y
5. Brilot AF
6. Grigorieff N
7. Korostelev AA
(2016) 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).

http://www.rcsb.org/pdb/explore/explore.do?structureId=5KPX
1. Loveland AB
2. Bah E
3. Madireddy R
4. Zhang Y
5. Brilot AF
6. Grigorieff N
7. Korostelev AA
(2016) RelA bound to 70S ribosome in absence of A/R tRNA (Structure I)
EMD-8279.

http://emsearch.rutgers.edu/atlas/8279_summary.html
1. Loveland AB
2. Bah E
3. Madireddy R
4. Zhang Y
5. Brilot AF
6. Grigorieff N
7. Korostelev AA
(2016) RelA bound to 70S ribosome in presence of A/R tRNA (Structure II)
EMD-8280.

http://emsearch.rutgers.edu/atlas/8280_summary.html
1. Loveland AB
2. Bah E
3. Madireddy R
4. Zhang Y
5. Brilot AF
6. Grigorieff N
7. Korostelev AA
(2016) RelA bound to 70S ribosome in presence of A/R tRNA (Structure III)
EMD-8281.

http://emsearch.rutgers.edu/atlas/8281_summary.html
1. Loveland AB
2. Bah E
3. Madireddy R
4. Zhang Y
5. Brilot AF
6. Grigorieff N
7. Korostelev AA
(2016) RelA bound to 70S ribosome in presence of A/R tRNA (Structure IV)
EMD-8282.

http://emsearch.rutgers.edu/atlas/8282_summary.html

Article and author information

Author details

Anna B Loveland

RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States

Competing interests
No competing interests declared.
Eugene Bah

Mayo Medical School, Rochester, United States

Competing interests
No competing interests declared.
Rohini Madireddy

RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States

Competing interests
No competing interests declared.
Ying Zhang

RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States

Competing interests
No competing interests declared.
Axel F Brilot

Department of Biochemistry, Brandeis University, Waltham, United States

Competing interests
No competing interests declared.
Nikolaus Grigorieff

Department of Biochemistry, Brandeis University, Waltham, United States

For correspondence
niko@grigorieff.org

Competing interests
Nikolaus Grigorieff, Reviewing editor, eLife.

"This ORCID iD identifies the author of this article:" 0000-0002-1506-909X
Andrei A Korostelev

RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States

For correspondence
andrei.korostelev@umassmed.edu

Competing interests
No competing interests declared.

"This ORCID iD identifies the author of this article:" 0000-0003-1588-717X

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.

Copyright

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.