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RS domain–splicing signal interactions in splicing of U12-type and U2-type introns

Abstract

Serine-arginine (SR) proteins are general metazoan splicing factors that contain an essential arginine/serine-rich (RS) domain. On typical U2-type introns, RS domains contact the branchpoint and 5′ splice site to promote base-pairing with U small nuclear RNAs (snRNAs). Here we analyze the role of SR proteins in splicing of U12-type introns and in the second step of U2-type intron splicing. We show that RS domains contact the branchpoint and 5′ splice site of a U12-type intron. On a U2-type intron, we find that the RS domain contacts the site of the U6 snRNA–5′ splice site interaction during the first step of splicing and shifts to contact the site of the U5 snRNA–exon 1 interaction during the second step. Our results reveal alternative interactions between the RS domain and 5′ splice site region that coincide with remodeling of the spliceosome between the two catalytic steps.

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Figure 1: The RS domain contacts the 5′ splice site and branchpoint of a U12-type intron.
Figure 2: The second step of splicing a U2-type intron requires an RS domain, which contacts the 5′ splice site region.
Figure 3: The RS domain–5′ splice site interaction occurs during the second step.
Figure 4: The interaction between the RS domain and 5′ splice site region shifts between the first and second steps of U2-type intron splicing.
Figure 5: During the second step of splicing, the RS domain contacts the pre-mRNA at the site of the U5 snRNA–exon 1 interaction.

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Acknowledgements

We thank A. Krainer (Cold Spring Harbor Laboratory) for providing plasmids pSP64-P120, pET19b-SF2/ASF-RRM/ψRRM and pET19b-SF2/ASF-RG, G. Akusjarvi (Uppsala University) for providing plasmids pET15b-MS2 and pET15b-MS2-RBD1, and Sara Evans for editorial assistance. This work was supported in part by a Charles A. King Trust Fellowship to H.S. and a US National Institutes of Health grant to M.R.G. M.R.G. is an investigator of the Howard Hughes Medical Institute.

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H.S. and M.R.G. designed the experiments, and H.S. performed all experiments. H.S. and M.R.G. interpreted the data and prepared the manuscript.

Note: Supplementary information is available on the Nature Structural & Molecular Biology website.

Corresponding author

Correspondence to Michael R Green.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Fig. 1

Splicing of the unimolecular counterpart of the bimolecular substrate is dependent upon addition of MS2-(ASF)RS. (PDF 281 kb)

Supplementary Fig. 2

On a conventional pre-mRNA substrate, the U5 snRNA-exon 1 interaction occurs prior to catalysis. (PDF 301 kb)

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Shen, H., Green, M. RS domain–splicing signal interactions in splicing of U12-type and U2-type introns. Nat Struct Mol Biol 14, 597–603 (2007). https://doi.org/10.1038/nsmb1263

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