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Assembly landscape for the bacterial large ribosomal subunit

Author

Listed:
  • Kai Sheng

    (The Scripps Research Institute)

  • Ning Li

    (The Scripps Research Institute)

  • Jessica N. Rabuck-Gibbons

    (The Scripps Research Institute
    The Salk Institute for Biological Studies)

  • Xiyu Dong

    (The Scripps Research Institute)

  • Dmitry Lyumkis

    (The Scripps Research Institute
    The Salk Institute for Biological Studies
    University of California San Diego)

  • James R. Williamson

    (The Scripps Research Institute)

Abstract

Assembly of ribosomes in bacteria is highly efficient, taking ~2-3 min, but this makes the abundance of assembly intermediates very low, which is a challenge for mechanistic understanding. Genetic perturbations of the assembly process create bottlenecks where intermediates accumulate, facilitating structural characterization. We use cryo-electron microscopy, with iterative subclassification to identify intermediates in the assembly of the 50S ribosomal subunit from E. coli. The analysis of the ensemble of intermediates that spans the entire biogenesis pathway for the 50 S subunit was facilitated by a dimensionality reduction and cluster picking approach using PCA-UMAP-HDBSCAN. The identity of the cooperative folding units in the RNA with associated proteins is revealed, and the hierarchy of these units reveals a complete assembly map for all RNA and protein components. The assembly generally proceeds co-transcriptionally, with some flexibility in the landscape to ensure efficiency for this central cellular process under a variety of growth conditions.

Suggested Citation

  • Kai Sheng & Ning Li & Jessica N. Rabuck-Gibbons & Xiyu Dong & Dmitry Lyumkis & James R. Williamson, 2023. "Assembly landscape for the bacterial large ribosomal subunit," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-40859-w
    DOI: 10.1038/s41467-023-40859-w
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    References listed on IDEAS

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    1. Zahra Assur Sanghai & Linamarie Miller & Kelly R. Molloy & Jonas Barandun & Mirjam Hunziker & Malik Chaker-Margot & Junjie Wang & Brian T. Chait & Sebastian Klinge, 2018. "Modular assembly of the nucleolar pre-60S ribosomal subunit," Nature, Nature, vol. 556(7699), pages 126-129, April.
    2. Konstantin Bokov & Sergey V. Steinberg, 2009. "A hierarchical model for evolution of 23S ribosomal RNA," Nature, Nature, vol. 457(7232), pages 977-980, February.
    3. Bo Qin & Simon M. Lauer & Annika Balke & Carlos H. Vieira-Vieira & Jörg Bürger & Thorsten Mielke & Matthias Selbach & Patrick Scheerer & Christian M. T. Spahn & Rainer Nikolay, 2023. "Cryo-EM captures early ribosome assembly in action," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
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    Cited by:

    1. Bintao He & Fa Zhang & Chenjie Feng & Jianyi Yang & Xin Gao & Renmin Han, 2024. "Accurate global and local 3D alignment of cryo-EM density maps using local spatial structural features," Nature Communications, Nature, vol. 15(1), pages 1-15, December.

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