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Kinetic redistribution of native and misfolded RNAs by a DEAD-box chaperone

Abstract

DExD/H-box proteins are ubiquitously involved in RNA-mediated processes and use ATP to accelerate conformational changes in RNA. However, their mechanisms of action, and what determines which RNA species are targeted, are not well understood. Here we show that the DExD/H-box protein CYT-19, a general RNA chaperone, mediates ATP-dependent unfolding of both the native conformation and a long-lived misfolded conformation of a group I catalytic RNA with efficiencies that depend on the stabilities of the RNA species but not on specific structural features. CYT-19 then allows the RNA to refold, changing the distribution from equilibrium to kinetic control. Because misfolding is favoured kinetically, conditions that allow unfolding of the native RNA yield large increases in the population of misfolded species. Our results suggest that DExD/H-box proteins act with sufficient breadth and efficiency to allow structured RNAs to populate a wider range of conformations than would be present at equilibrium. Thus, RNAs may face selective pressure to stabilize their active conformations relative to inactive ones to avoid significant redistribution by DExD/H-box proteins. Conversely, RNAs whose functions depend on forming multiple conformations may rely on DExD/H-box proteins to increase the populations of less stable conformations, thereby increasing their overall efficiencies.

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Figure 1: Unfolding of native and misfolded Tetrahymena ribozyme.
Figure 2: Secondary structure, long-range tertiary contacts, and mutations of the Tetrahymena ribozyme.
Figure 3: Unfolding of destabilized ribozyme variants.
Figure 4: Model for chaperone activity.

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Acknowledgements

We thank P. Tijerina and J. Grohman for purification of CYT-19; R. Coon for purification of CYT-18; D. Herschlag and A. Lambowitz for discussions and comments on the manuscript; and K. Johnson for sharing an unpublished version of the simulation program Kinetic Explorer. This work was funded by grants from the Welch Foundation and the National Institutes of Health (to R.R.).

Author Contributions H.B. performed the experiments; R.R. and H.B. designed the study, interpreted results, and wrote the paper.

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Correspondence to Rick Russell.

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Bhaskaran, H., Russell, R. Kinetic redistribution of native and misfolded RNAs by a DEAD-box chaperone. Nature 449, 1014–1018 (2007). https://doi.org/10.1038/nature06235

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