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S16 throws a conformational switch during assembly of 30S 5′ domain

Abstract

Rapid and accurate assembly of new ribosomal subunits is essential for cell growth. Here we show that the ribosomal proteins make assembly more cooperative by discriminating against non-native conformations of the Escherichia coli 16S ribosomal RNA. We used hydroxyl radical footprinting to measure how much the proteins stabilize individual ribosomal RNA tertiary interactions, revealing the free-energy landscape for assembly of the 16S 5′ domain. When ribosomal proteins S4, S17 and S20 bind the 5′ domain RNA, a native and a non-native assembly intermediate are equally populated. The secondary assembly protein S16 suppresses the non-native intermediate, smoothing the path to the native complex. In the final step of 5′ domain assembly, S16 drives a conformational switch at helix 3 that stabilizes pseudoknots in the 30S decoding center. Long-range communication between the S16 binding site and the decoding center helps to explain the crucial role of S16 in 30S assembly.

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Figure 1: Structure of the E. coli 5′ domain.
Figure 2: Hydroxyl radical footprinting of the 5′ domain in the presence and absence of proteins.
Figure 3: Global stabilization of rRNA tertiary structure by ribosomal proteins.
Figure 4: Primary assembly proteins pre-organize the S16 binding site.
Figure 5: S16 discriminates against non-native assembly intermediates.
Figure 6: RNA conformational changes during assembly.
Figure 7: Model for assembly of the 30S 5′ domain.

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Acknowledgements

The authors thank G. Culver (Univ. Rochester) and D. Draper, R. Moss and T. Adilakshmi (Johns Hopkins Univ. (JHU)) for gifts of plasmids and T. Adilakshmi, A. Cukras, J. Brunelle (JHU) and R. Green (JHU and Howard Hughes Medical Institute) for their help and advice. This work was supported by a grant from the US National Institutes of Health (GM60819).

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P.R. performed experiments, analyzed and interpreted data and wrote the paper; S.A.W. conceived the project, interpreted the data and wrote the paper.

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Correspondence to Sarah A Woodson.

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Ramaswamy, P., Woodson, S. S16 throws a conformational switch during assembly of 30S 5′ domain. Nat Struct Mol Biol 16, 438–445 (2009). https://doi.org/10.1038/nsmb.1585

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