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Shape-specific recognition in the structure of the Vts1p SAM domain with RNA

Nature Structural & Molecular Biology volume 13, pages 160–167 (2006)Cite this article

Abstract

Although the abundant sterile alpha motif (SAM) domain was originally classified as a protein-protein interaction domain, it has recently been shown that certain SAM domains have the ability to bind RNA, defining a new type of post-transcriptional gene regulator. To further understand the function of SAM-RNA recognition, we determined the solution structures of the SAM domain of the Saccharomyces cerevisiae Vts1p (Vts1p-SAM) and the Smaug response element (SRE) stem-loop RNA as a complex and in isolation. The structures show that Vts1p-SAM recognizes predominantly the shape of the SRE rather than its sequence, with the exception of a G located at the tip of the pentaloop. Using microarray gene profiling, we identified several genes in S. cerevisiae that seem to be regulated by Vts1p and contain one or more copies of the SRE.

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Figure 1: Domain structure of Vts1p-SAM, secondary structure of the SRE RNA and chemical shift difference mapping upon formation of the complex.
Figure 2: Structure of the free Vts1p-SAM domain and of the free SRE RNA.
Figure 3: Solution structure of Vts1p-SAM domain bound to SRE RNA and molecular basis of the recognition.
Figure 4: Genomic search for natural Vts1p substrates.
Figure 5: Comparison of the Vts1p-SAM–SRE complex with the structures of other SAM domain–containing proteins.

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Gene Expression Omnibus

Protein Data Bank

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GenBank/EMBL/DDBJ

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Acknowledgements

We are grateful to Y. Barral, Institute of Biochemistry, Swiss Federal Institute of Technology in Zurich, for providing the yeast genomic DNA for cloning and to S. Pitsch, L. Reymond and P. Wenter, Ecole Polytechnique Fédérale de Lausanne, for chemical synthesis of the 13C sugar-labeled RNAs. We thank the University of California at Los Angeles Microarray Core Facility for help with microarray experiments. This investigation was supported by a predoctoral fellowship from the Roche Research Foundation for Biology to F.C.O., the American Heart Association Western States Affiliate (A.L.), a Human Frontier Science Program postdoctoral fellowship to R.S., a US National Science Foundation IGERT DGE grant to M.J., US National Institutes of Health grant GM 61518 to G.C. and grants from the Swiss National Science Foundation, the Structural Biology National Center of Competence in Research and the Roche Research Fund for Biology at the Swiss Federal Institute of Technology in Zurich to F.H.-T.A. F.H.-T.A. is a European Molecular Biology Organization Young Investigator.

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Authors and Affiliations

  1. Institute for Molecular Biology and Biophysics, ETH Zürich, Zurich, CH-8093, Switzerland

    Florian C Oberstrass, Richard Stefl & Frédéric H-T Allain

  2. Department of Chemistry and Biochemistry, University of California at Los Angeles, Box 951569, 607 Charles E. Young Drive East, Los Angeles, 90095-1569, California, USA

    Albert Lee, Michael Janis & Guillaume Chanfreau

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Correspondence to Frédéric H-T Allain.

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Supplementary information

Supplementary Fig. 1

Chemical shift differences upon complexation of Vts1p-SAM and the SRE RNA. (PDF 489 kb)

Supplementary Fig. 2

Structure ensembles of the free Vts1p-SAM domain, the free RNA and their complex. (PDF 3429 kb)

Supplementary Fig. 3

13C-1H HSQC spectra of two sugar-labeled SRE RNAs in their bound state. (PDF 1090 kb)

Supplementary Fig. 4

Binding studies of mutant SRE RNAs. (PDF 879 kb)

Supplementary Fig. 5

Extended list of potential Vts1p binding targets found in strongly upregulated transcripts in the vts1Δ strain. (PDF 366 kb)

Supplementary Fig. 6

Conservation of predicted Vts1p-binding sites in closely related yeast species. (PDF 396 kb)

Supplementary Table 1

Transcripts found to be strongly upregulated in the vts1Δ strain. (PDF 48 kb)

Supplementary Table 2

Frequency of occurrence of computationally predicted Vts1p-target stem-loops in S. cerevisiae genomic ORF sequences and in sequences from the set of genes upregulated in the vts1Δ strain. (PDF 22 kb)

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Oberstrass, F., Lee, A., Stefl, R. et al. Shape-specific recognition in the structure of the Vts1p SAM domain with RNA. Nat Struct Mol Biol 13, 160–167 (2006). https://doi.org/10.1038/nsmb1038

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