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Sequence-specific recognition of RNA hairpins by the SAM domain of Vts1p

Nature Structural & Molecular Biology volume 13, pages 168–176 (2006)Cite this article

Abstract

The SAM domain of the Saccharomyces cerevisiae post-transcriptional regulator Vts1p epitomizes a subfamily of SAM domains conserved from yeast to humans that function as sequence-specific RNA-binding domains. Here we report the 2.0-Å X-ray structure of the Vts1p SAM domain bound to a high-affinity RNA ligand. Specificity of RNA binding arises from the association of a guanosine loop base with a shallow pocket on the SAM domain and from multiple SAM domain contacts to the unique backbone structure of the loop, defined in part by a nonplanar base pair within the loop. We have validated NNF1 as an endogenous target of Vts1p among 79 transcripts that copurify with Vts1p. Bioinformatic analysis of these mRNAs demonstrates that the RNA-binding specificity of Vts1p in vivo is probably more stringent than that of the isolated SAM domain in vitro.

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Figure 1: Biochemical and structural analysis of SRE binding by Vts1p-SAM.
Figure 2: The SRE pentaloop structure exhibits similarity to the UNCG and SECIS loops.
Figure 3: Features of the Vts1p-SAM–RNA binding interface.
Figure 4: Summary of fluorescence polarization binding measurements of Vts1p-SAM to SRE pentaloop variants bearing natural and synthetic substitutions.
Figure 5: Full-length Vts1p shows greater RNA-binding specificity than the isolated SAM domain.
Figure 6: The SRE consensus CNGG(N)n is prevalent among a population of putative Vts1p targets in yeast.

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Acknowledgements

We wish to thank M. Tyers and P. Jorgensen for assistance with microarray analyses and R. Collins and B. Derry for critical reading of the manuscript. This work was supported by operating grants to F.S. from the Canadian Institutes for Health Research and to C.A.S. from the National Cancer Institute of Canada with funds from the Terry Fox Run. F.S. is the recipient of a National Cancer Institute of Canada Scientist award.

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Authors and Affiliations

  1. Program in Molecular Biology and Cancer, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Ave., Toronto, M5G 1X5, Ontario, Canada

    Tzvi Aviv, Zhen Lin, Giora Ben-Ari & Frank Sicheri

  2. Department of Molecular and Medical Genetics, University of Toronto, Toronto, M5S 1A8, Ontario, Canada

    Tzvi Aviv & Frank Sicheri

  3. Department of Biochemistry, University of Toronto, Toronto, M5S 1A8, Ontario, Canada

    Craig A Smibert

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Correspondence to Frank Sicheri.

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Supplementary information

Supplementary Fig. 1

SAM domain recognition of the SRE is conserved across eukaryotes (PDF 588 kb)

Supplementary Fig. 2

Packing interactions in the crystal structure (PDF 365 kb)

Supplementary Fig. 3

Representative 2Fo – Fc electron density map highlights the disorder state of loop position 5 (PDF 508 kb)

Supplementary Fig. 4

Identifying Vts1 targets by microarray analysis (PDF 77 kb)

Supplementary Fig. 5

Binding of 6- and 7-base SRE loops to wild-type Vts1p using a gel shift assay (PDF 106 kb)

Supplementary Table 1

RNA determinants for SAM domain binding (PDF 65 kb)

Supplementary Table 2

Putative Vts1 targets in yeast identified by microarray analysis (PDF 155 kb)

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Aviv, T., Lin, Z., Ben-Ari, G. et al. Sequence-specific recognition of RNA hairpins by the SAM domain of Vts1p. Nat Struct Mol Biol 13, 168–176 (2006). https://doi.org/10.1038/nsmb1053

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