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Structure of the Bacillus subtilis 70S ribosome reveals the basis for species-specific stalling

Author

Listed:
  • Daniel Sohmen

    (University of Munich)

  • Shinobu Chiba

    (Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku)

  • Naomi Shimokawa-Chiba

    (Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku)

  • C. Axel Innis

    (Institut Européen de Chimie et Biologie, Université de Bordeaux
    Institut National de la Santé et de la Recherche Médicale (U869))

  • Otto Berninghausen

    (University of Munich)

  • Roland Beckmann

    (University of Munich
    Center for integrated Protein Science Munich (CiPSM), University of Munich)

  • Koreaki Ito

    (Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku)

  • Daniel N. Wilson

    (University of Munich
    Center for integrated Protein Science Munich (CiPSM), University of Munich)

Abstract

Ribosomal stalling is used to regulate gene expression and can occur in a species-specific manner. Stalling during translation of the MifM leader peptide regulates expression of the downstream membrane protein biogenesis factor YidC2 (YqjG) in Bacillus subtilis, but not in Escherichia coli. In the absence of structures of Gram-positive bacterial ribosomes, a molecular basis for species-specific stalling has remained unclear. Here we present the structure of a Gram-positive B. subtilis MifM-stalled 70S ribosome at 3.5–3.9 Å, revealing a network of interactions between MifM and the ribosomal tunnel, which stabilize a non-productive conformation of the PTC that prevents aminoacyl-tRNA accommodation and thereby induces translational arrest. Complementary genetic analyses identify a single amino acid within ribosomal protein L22 that dictates the species specificity of the stalling event. Such insights expand our understanding of how the synergism between the ribosome and the nascent chain is utilized to modulate the translatome in a species-specific manner.

Suggested Citation

  • Daniel Sohmen & Shinobu Chiba & Naomi Shimokawa-Chiba & C. Axel Innis & Otto Berninghausen & Roland Beckmann & Koreaki Ito & Daniel N. Wilson, 2015. "Structure of the Bacillus subtilis 70S ribosome reveals the basis for species-specific stalling," Nature Communications, Nature, vol. 6(1), pages 1-10, November.
    • Handle: RePEc:nat:natcom:v:6:y:2015:i:1:d:10.1038_ncomms7941
    DOI: 10.1038/ncomms7941
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    Cited by:

    1. Keigo Fujiwara & Naoko Tsuji & Mayu Yoshida & Hiraku Takada & Shinobu Chiba, 2024. "Patchy and widespread distribution of bacterial translation arrest peptides associated with the protein localization machinery," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    2. Martino Morici & Sara Gabrielli & Keigo Fujiwara & Helge Paternoga & Bertrand Beckert & Lars V. Bock & Shinobu Chiba & Daniel N. Wilson, 2024. "RAPP-containing arrest peptides induce translational stalling by short circuiting the ribosomal peptidyltransferase activity," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    3. Felix Gersteuer & Martino Morici & Sara Gabrielli & Keigo Fujiwara & Haaris A. Safdari & Helge Paternoga & Lars V. Bock & Shinobu Chiba & Daniel N. Wilson, 2024. "The SecM arrest peptide traps a pre-peptide bond formation state of the ribosome," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    4. Laura Czech & Christopher-Nils Mais & Hanna Kratzat & Pinku Sarmah & Pietro Giammarinaro & Sven-Andreas Freibert & Hanna Folke Esser & Joanna Musial & Otto Berninghausen & Wieland Steinchen & Roland B, 2022. "Inhibition of SRP-dependent protein secretion by the bacterial alarmone (p)ppGpp," Nature Communications, Nature, vol. 13(1), pages 1-14, December.

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