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Role of the ubiquitin-like protein Hub1 in splice-site usage and alternative splicing

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Abstract

Alternative splicing of pre-messenger RNAs diversifies gene products in eukaryotes and is guided by factors that enable spliceosomes to recognize particular splice sites. Here we report that alternative splicing of Saccharomyces cerevisiae SRC1 pre-mRNA is promoted by the conserved ubiquitin-like protein Hub1. Structural and biochemical data show that Hub1 binds non-covalently to a conserved element termed HIND, which is present in the spliceosomal protein Snu66 in yeast and mammals, and Prp38 in plants. Hub1 binding mildly alters spliceosomal protein interactions and barely affects general splicing in S. cerevisiae. However, spliceosomes that lack Hub1, or are defective in Hub1–HIND interaction, cannot use certain non-canonical 5′ splice sites and are defective in alternative SRC1 splicing. Hub1 confers alternative splicing not only when bound to HIND, but also when experimentally fused to Snu66, Prp38, or even the core splicing factor Prp8. Our study indicates a novel mechanism for splice site utilization that is guided by non-covalent modification of the spliceosome by an unconventional ubiquitin-like modifier.

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Figure 1: Hub1 binds to HIND.
Figure 2: Functional links to splicing.
Figure 3: Splice-site usage.
Figure 4: Alternative splicing of SRC1.

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Change history

  • 09 June 2011

    Figs 3c and 4b were corrected.

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Acknowledgements

We thank U. Cramer and M. Kost for technical assistance, G. Dittmar, C. Guthrie, M. Konarska, K. Matuschewski, O. Nielsen, M. Rosbash and H. Yashiroda for materials, S. Uebel and C. Boulegue for mass spectrometric analysis and help, K. Hofmann for pointing out putative HIND elements in Prp38 proteins of plants, and M. Singh for initiating structural work. S.J. is supported by the Max Planck Society, Deutsche Forschungsgemeinschaft, Fonds der chemischen Industrie, Center for Integrated Protein Science Munich and RUBICON EU Network of Excellence; T.A.H. by the Max Planck Society; M.A. by NIH (GM040478).

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Authors

Contributions

S.K.M. (S. cerevisiae, S. pombe), T.A. (mammalian) and S.J. designed, obtained and analysed the genetic, biochemical and functional data; G.M.P, M.K. and T.A.H. the structural data; R.J.N. and M.A. Jr the splicing array data. S.J. and S.K.M. wrote the paper, and all authors contributed to the manuscript.

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Correspondence to Stefan Jentsch.

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The authors declare no competing financial interests.

Additional information

Coordinates and the experimental structural factors of both complexes have been deposited in the PDB under the following codes: Hub1–HIND-I, 3PLU; Hub1–HIND-II, 3PLV.

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This file contains Supplementary Figures 1-14 with legends, Supplementary Tables 1-3 and additional references. (PDF 7396 kb)

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Mishra, S., Ammon, T., Popowicz, G. et al. Role of the ubiquitin-like protein Hub1 in splice-site usage and alternative splicing. Nature 474, 173–178 (2011). https://doi.org/10.1038/nature10143

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