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Alternate rRNA secondary structures as regulators of translation

Abstract

Structural dynamics of large molecular assemblies are intricately linked to function. For ribosomes, macromolecular changes occur especially during mRNA translation and involve participation of ribosomal RNA. Without suitable probes specific to RNA secondary structure, however, elucidation of more subtle dynamic ribosome structure-function relationships, especially in vivo, remains challenging. Here we report that the Z-DNA– and Z-RNA–binding domain Zα, derived from the human RNA editing enzyme ADAR1-L, binds with high stability to specific rRNA segments of Escherichia coli and human ribosomes. Zα impaired in Z-RNA recognition does not associate with ribosomes. Notably, ZαADAR1-ribosome interaction blocks translation in vitro and in vivo, with substantial physiological consequences. Our study shows that ribosomes can be targeted by a protein that specifically recognizes an alternate rRNA secondary structure, and suggests a new mechanism of translational regulation on the ribosome.

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Figure 1: Association of ZαADAR1 with E. coli rRNA in vivo.
Figure 2: Identification of hcRBSs for ZαADAR1 on E. coli ribosomes.
Figure 3: Inhibition of E. coli translation by ZαADAR1 in vitro and in vivo.
Figure 4: ZαADAR1 binding to human rRNA segments.
Figure 5: Inhibition of eukaryotic translation by ZαADAR1.

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Acknowledgements

We thank A. Rich (Massachusetts Institute of Technology) for expression vectors. We thank X. Lin for confirming results on delay from exit from lag phase in ZαADAR1 cells. This work was funded by Academic Research Council (Singapore) grants 12/05 (P.D.) and T207B3205 (K.P.). We also acknowledge funding of graduate scholarships by the Singapore Ministry of Education.

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S.F. and H.L. designed and carried out biochemical and cell biological research; J.Z. and K.P. carried out NMR and CD analyses; K.L. provided material and input on the manuscript; T.U.S. contributed ideas and analyzed data; P.D. designed and supervised research, analyzed data and wrote the paper.

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Correspondence to Peter Dröge.

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Supplementary Figures 1–11 and Supplementary Table 1 (PDF 2339 kb)

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Feng, S., Li, H., Zhao, J. et al. Alternate rRNA secondary structures as regulators of translation. Nat Struct Mol Biol 18, 169–176 (2011). https://doi.org/10.1038/nsmb.1962

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