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Intermolecular domain swapping induces intein-mediated protein alternative splicing

Nature Chemical Biology volume 9, pages 616–622 (2013)Cite this article

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Abstract

Protein sequences are diversified on the DNA level by recombination and mutation and can be further increased on the RNA level by alternative RNA splicing, involving introns that have important roles in many biological processes. The protein version of introns (inteins), which catalyze protein splicing, were first reported in the 1990s. The biological roles of protein splicing still remain elusive because inteins neither provide any clear benefits nor have an essential role in their host organisms. We now report protein alternative splicing, in which new protein sequences can be produced by protein recombination by intermolecular domain swapping of inteins, as elucidated by NMR spectroscopy and crystal structures. We demonstrate that intein-mediated protein alternative splicing could be a new strategy to increase protein diversity (that is, functions) without any modification in genetic backgrounds. We also exploited it as a post-translational protein conformation–driven switch of protein functions (for example, as highly specific protein interference).

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Figure 1: Protein splicing in cis and trans and iPAS.
Figure 2: Structural basis of iPAS by NMR spectroscopy and X-ray crystallography.
Figure 3: iPAS without split inteins.
Figure 4: Factors influencing iPAS.
Figure 5: Modulation of GFP fluorescence by the conformation-driven switch.

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Acknowledgements

This work was supported by the Academy of Finland (131413 and 137995) and the Sigrid Jusélius Foundation and Biocenter Finland (to H.I., for crystallization, MS and NMR facilities at the Institute of Biotechnology). A.S.A. and J.S.O. acknowledge Viikki Doctoral Programme in Molecular Biosciences and the National Doctoral Programme in Informational and Structural Biology for financial support, respectively. The authors thank G. Volkmann for his help at the very early stage of the project. The authors also thank F. Perler for providing us with the latest InBase data set and S. Ferkau and C. Albert for their technical support.

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  1. Research Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Helsinki, Finland

    A Sesilja Aranko, Jesper S Oeemig, Tommi Kajander & Hideo Iwaï

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  1. A Sesilja Aranko
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  2. Jesper S Oeemig
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Contributions

A.S.A. and H.I. designed and performed experiments, analyzed data and prepared the manuscript; T.K., J.S.O. and H.I. performed crystallographic experiments and analyzed diffraction data; H.I. and J.S.O. performed NMR measurements and analyzed NMR data.

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Correspondence to Hideo Iwaï.

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Aranko, A., Oeemig, J., Kajander, T. et al. Intermolecular domain swapping induces intein-mediated protein alternative splicing. Nat Chem Biol 9, 616–622 (2013). https://doi.org/10.1038/nchembio.1320

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