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Structure of a hibernating 100S ribosome reveals an inactive conformation of the ribosomal protein S1

Nature Microbiology volume 3, pages 1115–1121 (2018)Cite this article

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Abstract

To survive under conditions of stress, such as nutrient deprivation, bacterial 70S ribosomes dimerize to form hibernating 100S particles1. In γ-proteobacteria, such as Escherichia coli, 100S formation requires the ribosome modulation factor (RMF) and the hibernation promoting factor (HPF)2,3,4. Here we present single-particle cryo-electron microscopy structures of hibernating 70S and 100S particles isolated from stationary-phase E. coli cells at 3.0 Å and 7.9 Å resolution, respectively. The structures reveal the binding sites for HPF and RMF as well as the unexpected presence of deacylated E-site transfer RNA and ribosomal protein bS1. HPF interacts with the anticodon-stem-loop of the E-tRNA and occludes the binding site for the messenger RNA as well as A- and P-site tRNAs. RMF facilitates stabilization of a compact conformation of bS1, which together sequester the anti-Shine-Dalgarno sequence of the 16S ribosomal RNA (rRNA), thereby inhibiting translation initiation. At the dimerization interface, the C-terminus of uS2 probes the mRNA entrance channel of the symmetry-related particle, thus suggesting that dimerization inactivates ribosomes by blocking the binding of mRNA within the channel. The back-to-back E. coli 100S arrangement is distinct from 100S particles observed previously in Gram-positive bacteria5,6,7,8, and reveals a unique role for bS1 in translation regulation.

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Fig. 1: Cryo-EM structure of the hibernating 70S ribosome.
Fig. 2: Interaction of HPF and RMF on the 30S subunit.
Fig. 3: Conformation and interaction of bS1 on the hibernating 70S.
Fig. 4: Cryo-EM structure of the hibernating 100S particle.

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Acknowledgements

We thank S. Rieder and C. Ungewickell for expert technical assistance and C. Schmidt for IT support. This research was supported by grants from the Deutsche Forschungsgemeinschaft SPP1879 (to D.N.W), CZ234/1–1 (to A.C.), FOR1805 (to D.N.W., Z.I. and R.B.).

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Author notes

  1. These authors contributed equally: B. Beckert, M. Turk.

Authors and Affiliations

  1. Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany

    Bertrand Beckert, Andreas Czech, Zoya Ignatova & Daniel N. Wilson

  2. Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany

    Martin Turk & Jürgen M. Plitzko

  3. Gene Center, Department of Biochemistry and Center for integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Munich, Germany

    Otto Berninghausen & Roland Beckmann

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Contributions

D.N.W. designed the study. B.B. prepared the cryo-EM sample. O.B. collected the single-particle cryo-EM data, which was processed by B.B. The tilt data were collected and processed by M.T. A.C. performed the microarray analysis. B.B. built and refined the molecular models and generated the figures. B.B., M.T., R.B., Z.I., J.P. and D.N.W. interpreted the results. B.B. and D.N.W. wrote the paper.

Corresponding authors

Correspondence to Jürgen M. Plitzko or Daniel N. Wilson.

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The authors declare no competing interests.

Data availability

Cryo-electron density maps of the hibernating 70S and 100S ribosomal particles are available through the EMDB with entry codes EMD-0137 and EMD-0139, respectively. Molecular models of the hibernating 70S and 100S ribosomal particles are deposited in the Protein Data Bank with entry code 6H4N and 6H58, respectively. The data that support the findings of this study are available from the corresponding authors on request.

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Supplementary information

Supplementary Information

Supplementary Figures 1–11, Supplementary Table 1.

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Supplementary Video 1

Overview of the cryo-EM maps for hibernating 70S and 100S particles.

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Beckert, B., Turk, M., Czech, A. et al. Structure of a hibernating 100S ribosome reveals an inactive conformation of the ribosomal protein S1. Nat Microbiol 3, 1115–1121 (2018). https://doi.org/10.1038/s41564-018-0237-0

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