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Molecular basis of purine-rich RNA recognition by the human SR-like protein Tra2-β1

Nature Structural & Molecular Biology volume 18, pages 443–450 (2011)Cite this article

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Abstract

Tra2-β1 is a unique splicing factor as its single RNA recognition motif (RRM) is located between two RS (arginine-serine) domains. To understand how this protein recognizes its RNA target, we solved the structure of Tra2-β1 RRM in complex with RNA. The central 5′-AGAA-3′ motif is specifically recognized by residues from the β-sheet of the RRM and by residues from both extremities flanking the RRM. The structure suggests that RNA binding by Tra2-β1 induces positioning of the two RS domains relative to one another. By testing the effect of Tra2-β1 and RNA mutations on the splicing of SMN2 exon 7, we validated the importance of the RNA-protein contacts observed in the structure for the function of Tra2-β1 and determined the functional sequence of Tra2-β1 in SMN2 exon 7. Finally, we propose a model for the assembly of multiple RNA binding proteins on this exon.

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Figure 1: Study of the interaction between Tra2-β1 RRM and the 5′-AAGAAC-3′ RNA by ITC and NMR.
Figure 2: Overview of the solution structure of Tra2-β1 RRM in complex with the 5′-AAGAAC-3′ RNA.
Figure 3: Effect of Tra2-β1 mutations on SMN2 exon 7 splicing.
Figure 4: Effect of nucleotide substitutions in the Tra2-β1 binding site on SMN2 exon 7 splicing.
Figure 5: Binding of Tra2-β1 RRM might induce the positioning of the two RS domains on SMN exon 7 or the recruitment of hnRNP G and SRp30c.

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Protein Data Bank

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GenBank/EMBL/DDBJ

Change history

  • 25 March 2011

    In the version of this article initially published online, in Figure 2c, the label "A1" in the right-hand panel was displaced to the left, and in the Results, "Tra2-β1" was incorrectly written as "Tra2-b1" in the subheading "Tra2-β1 binding to SMN might change position of RS domains." The errors have been corrected for all versions of this article.

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Acknowledgements

We thank J. Stevenin and D. Watt for reading the manuscript; J. Hall and M. Zimmermann for labeled RNA; the SNF-NCCR Structural Biology and EURASNET for financial support to F.H.-T.A.; the Muscular Dystrophy Association for support of S.S. and the European Molecular Biology Organization for a postdoctoral fellowship to A.C.

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Authors and Affiliations

  1. Institute for Molecular Biology and Biophysics, Swiss Federal Institute of Technology, Zürich, Switzerland

    Antoine Cléry, Sandrine Jayne, Cyril Dominguez & Frédéric H-T Allain

  2. Institute of Biochemistry, University of Erlangen-Nürnberg, Erlangen, Germany

    Natalya Benderska & Stefan Stamm

  3. Department of Molecular and Cellular Biochemistry, Biomedical Biological Sciences Research Building, University of Kentucky, Lexington, Kentucky, USA

    Stefan Stamm

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  1. Antoine Cléry
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Contributions

F.H.-T.A. and S.S. designed the project; A.C. prepared protein and RNA samples for structural studies; A.C., C.D. and F.H.-T.A. analyzed NMR data; A.C. and C.D. did structure calculations; S.J., N.B. and A.C. did in vivo splicing assays; A.C. and C.D. did ITC measurements; N.B. conducted the coimmunoprecipitation experiments; all authors discussed the results and wrote and approved the manuscript.

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Correspondence to Frédéric H-T Allain.

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Cléry, A., Jayne, S., Benderska, N. et al. Molecular basis of purine-rich RNA recognition by the human SR-like protein Tra2-β1. Nat Struct Mol Biol 18, 443–450 (2011). https://doi.org/10.1038/nsmb.2001

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