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Staufen1 dimerizes through a conserved motif and a degenerate dsRNA-binding domain to promote mRNA decay

Nature Structural & Molecular Biology volume 20, pages 515–524 (2013)Cite this article

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Abstract

Staufen1 (STAU1)-mediated mRNA decay (SMD) degrades mammalian-cell mRNAs that bind the double-stranded RNA (dsRNA)-binding protein STAU1 in their 3′ untranslated region. We report a new motif, which typifies STAU homologs from all vertebrate classes, that is responsible for human STAU1 (hSTAU1) homodimerization. Our crystal structure and mutagenesis analyses reveal that this motif, which we named the Staufen-swapping motif (SSM), and the dsRNA-binding domain 5 ('RBD'5) mediate protein dimerization: the two SSM α-helices of one molecule interact primarily through a hydrophobic patch with the two 'RBD'5 α-helices of a second molecule. 'RBD'5 adopts the canonical α-β-β-β-α fold of a functional RBD, but it lacks residues and features required to bind duplex RNA. In cells, SSM-mediated hSTAU1 dimerization increases the efficiency of SMD by augmenting hSTAU1 binding to the ATP-dependent RNA helicase hUPF1. Dimerization regulates keratinocyte-mediated wound healing and many other cellular processes.

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Figure 1: Comparison of vertebrate STAU sequences, and the X-ray crystal structure of hSTAU1 SSM-'RBD'5.
Figure 2: Comparison of hSTAU155 'RBD'5 with an RBD that binds dsRNA.
Figure 3: hSTAU155 SSM-'RBD'5 is a dimer in solution.
Figure 4: 'RBD'5 and SSM interact in trans, and expression of either one inhibits hSTAU1 dimerization and SMD.
Figure 5: Sequences C-terminal to 'RBD'5 α1 are not required for hSTAU155 dimerization, and dimerization promotes hUPF1 binding and SMD.
Figure 6: hSTAU155 point mutations that disrupt dimerization inhibit hUPF1 binding and SMD, thereby precluding contributions of SMD toward inhibiting cell motility.
Figure 7: Model for how hSTAU1 dimers recruit hUPF1 to the 3′ UTR of an mRNA that is targeted for SMD and promote its decay.

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Acknowledgements

We thank H. Kuzmiak (University of Rochester) for generating pSTAU155(R)-HA3; L. DesGroseillers (Université de Montréal) for pSTAU155-HA3; K. Nehrke for microscope use; G. Pavlencheva and C. Hull for technical assistance; R. Singer (Albert Einstein College of Medicine) for pmRFP; S. de Lucas and J. Ortín (Centro Nacional de Biotecnología) for anti-STAU1; and J. Lary (University of Connecticut Analytical Ultracentrifugation Facility), J. Jenkins, J. Wedekind and M. Popp for helpful conversations. This work was made possible by US National Institutes of Health (NIH) grant NIH R01 GM074593 to L.E.M. M.L.G. was supported by a Ruth L. Kirschstein National Research Service Award (NRSA) NIHF32 GM090479 Fellowship and grant NIH NCI T32 CA09363. C.G. was supported by a Messersmith Graduate Student Fellowship. The University of Rochester Medical Center Structural Biology and Biophysics Facility is supported by NIH National Center for Research Resources (NCRR) grants 1S10 RR026501 and 1S10 RR027241, NIH National Institute of Allergy and Infectious Diseases (NIAID) grant P30 AI078498 and the University of Rochester School of Medicine and Dentistry. The Cornell High Energy Synchrotron Source (CHESS) is supported by the National Science Foundation (NSF) and NIH National Institute of General Medicine Sciences (NIGMS) through NSF award DMR-0225180. Macromolecular Diffraction at CHESS (MacCHESS) is supported by NIH NCRR RR-01646. The Stanford Synchrotron Radiation Lightsource (SSRL) Structural Molecular Biology Program is supported by the Department of Energy Office of Biological and Environmental Research, the NIH National Center for Research Resources Biomedical Technology Program (P41RR001209) and the NIGMS.

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  1. Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York, USA

    Michael L Gleghorn, Chenguang Gong, Clara L Kielkopf & Lynne E Maquat

  2. Center for RNA Biology, University of Rochester, Rochester, New York, USA

    Michael L Gleghorn, Chenguang Gong, Clara L Kielkopf & Lynne E Maquat

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Contributions

M.L.G. and L.E.M. conceived the project and wrote the manuscript with input from C.L.K. Experiments were designed by M.L.G., C.G. and L.E.M. M.L.G. carried out the structural work with input from C.L.K., and designed and constructed the plasmids needed for this study. C.G. undertook experiments using cultured cells. All authors contributed to data interpretation.

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Correspondence to Lynne E Maquat.

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Gleghorn, M., Gong, C., Kielkopf, C. et al. Staufen1 dimerizes through a conserved motif and a degenerate dsRNA-binding domain to promote mRNA decay. Nat Struct Mol Biol 20, 515–524 (2013). https://doi.org/10.1038/nsmb.2528

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