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The RNA-binding SAM domain of Smaug defines a new family of post-transcriptional regulators

Nature Structural & Molecular Biology volume 10, pages 614–621 (2003)Cite this article

Abstract

Anteroposterior patterning in Drosophila melanogaster is dependent on the sequence-specific RNA-binding protein Smaug, which binds to and regulates the translation of nanos (nos) mRNA. Here we demonstrate that the sterile-α motif (SAM) domain of Smaug functions as an RNA-recognition domain. This represents a new function for the SAM domain family, which is well characterized for mediating protein-protein interactions. Using homology modeling and site-directed mutagenesis, we have localized the RNA-binding surface of the Smaug SAM domain and have elaborated the RNA consensus sequence required for binding. Residues that compose the RNA-binding surface are conserved in a subgroup of SAM domain–containing proteins, suggesting that the function of the domain is conserved from yeast to humans. We show here that the SAM domain of Saccharomyces cerevisiae Vts1 binds RNA with the same specificity as Smaug and that Vts1 induces transcript degradation through a mechanism involving the cytoplasmic deadenylase CCR4. Together, these results suggest that Smaug and Vts1 define a larger class of post-transcriptional regulators that act in part through a common transcript-recognition mechanism.

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Figure 1: Homology modeling of Smg SAM domain.
Figure 2: Protein determinants of the Smg and Vts1 SAM domains required for SRE binding.
Figure 3: RNA stem-loop determinants for binding to Smg and Vts1.
Figure 4: VTS1 regulates gene expression by destabilizing SRE-bearing transcripts.
Figure 5: VTS1 regulation of gene expression is CCR4 dependent.

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Acknowledgements

We thank J. Glover and M. Tyers for plasmids p413–GFP and FLAG–VTS1, respectively. We also thank D. Durocher and R. Collins for assistance with assay development and A. Willems for relating the similarity between the SSR1 domain of Smaug and the dimerization domain of βTRCP. We are grateful to P.S. Metalnikov and P. O'Donnel for assistance with mass spectrometry. C.A.S is supported by a Canadian Institutes of Health Research (CIHR) scholarship. F.S. is a Research Scientist of the National Cancer Institute of Canada (NCIC). This work was supported by operating grants from the CIHR and the NCIC with funds from the Terry Fox Run.

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

    Tzvi Aviv, Zhen Lin, Stefanie Lau & 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

    Laura M. Rendl & Craig A Smibert

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Correspondence to Frank Sicheri or Craig A Smibert.

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Aviv, T., Lin, Z., Lau, S. et al. The RNA-binding SAM domain of Smaug defines a new family of post-transcriptional regulators. Nat Struct Mol Biol 10, 614–621 (2003). https://doi.org/10.1038/nsb956

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