Assembly landscape for the bacterial large ribosomal subunit

Kai Sheng, Ning Li, Jessica N. Rabuck-Gibbons, Xiyu Dong, Dmitry Lyumkis and James R. Williamson ()
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Kai Sheng: The Scripps Research Institute
Ning Li: The Scripps Research Institute
Jessica N. Rabuck-Gibbons: The Scripps Research Institute
Xiyu Dong: The Scripps Research Institute
Dmitry Lyumkis: The Scripps Research Institute
James R. Williamson: The Scripps Research Institute

Nature Communications, 2023, vol. 14, issue 1, 1-10

Abstract: 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.

Date: 2023
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DOI: 10.1038/s41467-023-40859-w

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