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Structural and biochemical basis for misfolded RNA recognition by the Ro autoantigen

Nature Structural & Molecular Biology volume 13, pages 1002–1009 (2006)Cite this article

Abstract

The Ro autoantigen is ring-shaped, binds misfolded noncoding RNAs and is proposed to function in quality control. Here we determine how Ro interacts with misfolded RNAs. Binding of Ro to misfolded precursor (pre)-5S ribosomal RNA requires a single-stranded 3′ end and helical elements. As mutating most sequences of the helices and tail results in modest decreases in binding, Ro may be able to associate with a range of RNAs. Ro binds several other RNAs that contain single-stranded tails. A crystal structure of Ro bound to a misfolded pre-5S rRNA fragment reveals that the tail inserts into the cavity, while a helix binds on the surface. Most contacts of Ro with the helix are to the backbone. Mutagenesis reveals that Ro has an extensive RNA-binding surface. We propose that Ro uses this surface to scavenge RNAs that fail to bind their specific RNA-binding proteins.

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Figure 1: Regions of misfolded pre-5S rRNA that are protected or structurally altered by Ro binding.
Figure 2: Ro contacts the tail and several helices in misfolded pre-5S rRNA.
Figure 3: Ro binding requires helical elements and a single-stranded tail of at least 5 nt.
Figure 4: Interactions of Ro with a fragment of misfolded pre-5S RNA.
Figure 5: Ro binds other noncoding RNAs that contain a single-stranded tail.

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Acknowledgements

We thank A. Alexandrov, S. Sim, E. Ullu and E. Wurtmann for comments on the manuscript and S. Baserga (Yale University) and J. Steitz (Yale University) for gifts of plasmids. We are grateful to the staff at beamline X25 at the Brookhaven National Laboratory for assistance with data collection. A.J.S. was supported by a fellowship from the Arthritis Foundation. This work was funded by grants from the US National Institutes of Health (R01-GM073863 to S.L.W. and R01-GM70521 to K.M.R.) and the Pew Charitable Trust (to K.M.R.).

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  1. Adam J Stein

    Present address: Department of Biochemistry and Molecular Biology, Rosalind Franklin University of Medicine and Science, North Chicago, Illinois, 60064, USA

Authors and Affiliations

  1. Department of Cell Biology, Yale University School of Medicine, New Haven, 06510, Connecticut, USA

    Gabriele Fuchs, Adam J Stein, Chunmei Fu, Karin M Reinisch & Sandra L Wolin

  2. Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, 06510, Connecticut, USA

    Sandra L Wolin

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Correspondence to Karin M Reinisch or Sandra L Wolin.

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Supplementary information

Supplementary Fig. 1

Difference electron density maps for RNA. (PDF 1562 kb)

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Fuchs, G., Stein, A., Fu, C. et al. Structural and biochemical basis for misfolded RNA recognition by the Ro autoantigen. Nat Struct Mol Biol 13, 1002–1009 (2006). https://doi.org/10.1038/nsmb1156

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