Letter | Published:

Ribosome-dependent activation of stringent control

Nature 534, 277–280 (09 June 2016) | Download Citation

Subjects

Abstract

In order to survive, bacteria continually sense, and respond to, environmental fluctuations. Stringent control represents a key bacterial stress response to nutrient starvation1,2 that leads to rapid and comprehensive reprogramming of metabolic and transcriptional patterns3. In general, transcription of genes for growth and proliferation is downregulated, while those important for survival and virulence are upregulated4. Amino acid starvation is sensed by depletion of the aminoacylated tRNA pools5, and this results in accumulation of ribosomes stalled with non-aminoacylated (uncharged) tRNA in the ribosomal A site6,7. RelA is recruited to stalled ribosomes and activated to synthesize a hyperphosphorylated guanosine analogue, (p)ppGpp8, which acts as a pleiotropic secondary messenger. However, structural information about how RelA recognizes stalled ribosomes and discriminates against aminoacylated tRNAs is missing. Here we present the cryo-electron microscopy structure of RelA bound to the bacterial ribosome stalled with uncharged tRNA. The structure reveals that RelA utilizes a distinct binding site compared to the translational factors, with a multi-domain architecture that wraps around a highly distorted A-site tRNA. The TGS (ThrRS, GTPase and SpoT) domain of RelA binds the CCA tail to orient the free 3′ hydroxyl group of the terminal adenosine towards a β-strand, such that an aminoacylated tRNA at this position would be sterically precluded. The structure supports a model in which association of RelA with the ribosome suppresses auto-inhibition to activate synthesis of (p)ppGpp and initiate the stringent response. Since stringent control is responsible for the survival of pathogenic bacteria under stress conditions, and contributes to chronic infections and antibiotic tolerance, RelA represents a good target for the development of novel antibacterial therapeutics.

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Accessions

Primary accessions

Electron Microscopy Data Bank

Protein Data Bank

Data deposits

The maps have been deposited with the EMDB under accession codes 8107– 8115. Coordinates have been deposited with the Protein Data Bank under the accession code 5IQR.

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Acknowledgements

We thank A. Kelley for providing tRNAs, A. Xu and J. Murray for their contributions to the early stages of this project, C. G. Savva for help with data collection, J. Grimmett and T. Darling for computing support, and X. Bai, G. Murshudov, S. H. W. Scheres, and S. Tan for discussions. This work was supported by grants to V.R. from the UK Medical Research Council (MC_U105184332), the Wellcome Trust (WT096570), the Agouron Institute, and the Louis-Jeantet Foundation.

Author information

    • Israel S. Fernández

    Present address: Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA.

    • Alan Brown
    •  & Israel S. Fernández

    These authors contributed equally to this work

Affiliations

  1. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK

    • Alan Brown
    • , Israel S. Fernández
    • , Yuliya Gordiyenko
    •  & V. Ramakrishnan

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Contributions

A.B., I.S.F., and V.R. designed the study. Y.G. purified ribosomes. I.S.F. prepared samples, optimized conditions and collected data. A.B. processed data and interpreted the cryo-electron microscopy reconstructions. A.B., I.S.F., and V.R. wrote the manuscript. All authors discussed and commented on the final manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to V. Ramakrishnan.

Extended data

Extended data figures

  1. 1.

    In silico 3D classification scheme.

  2. 2.

    Quality of maps and models.

  3. 3.

    Examples of RelA density.

  4. 4.

    RelA domains are connected by flexible linkers.

  5. 5.

    The conformation of uncharged A-site tRNA in the presence of RelA is distinct from aminoacylated A/T-tRNA in the presence of EF-Tu.

  6. 6.

    RelA topology diagram.

  7. 7.

    RelA binds RNA through electropositive surfaces.

  8. 8.

    RelA contains an RNA recognition motif (RRM).

Extended data tables

  1. 1.

    Refinement and model statistics

  2. 2.

    Modelled residues

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DOI

https://doi.org/10.1038/nature17675

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