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Nat Microbiol. 2018 Oct;3(10):1115-1121. doi: 10.1038/s41564-018-0237-0. Epub 2018 Sep 3.

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

Author information

1
Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany.
2
Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany.
3
Gene Center, Department of Biochemistry and Center for integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Munich, Germany.
4
Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany. plitzko@biochem.mpg.de.
5
Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany. Daniel.wilson@chemie.uni-hamburg.de.

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)2-4. 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 bacteria5-8, and reveals a unique role for bS1 in translation regulation.

PMID:
30177741
DOI:
10.1038/s41564-018-0237-0

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