Abstract
The splicing factor SUP-12 from Caenorhabditis elegans binds to regulatory RNA elements in pre-mRNA in order to generate tissue-specific alternative splicing for genes such as the fibroblast growth factor receptor egl-15. In nematode muscle cells, SUP-12 promotes the use of a mutually exclusive exon to impart variant binding specificity to the EGL-15 extracellular protein domain. Here we report the side chain and backbone 1H, 13C and 15N chemical shift assignments for the bacterially expressed RNA recognition motif domain from SUP-12, both in isolation as well as bound to a short RNA derived from the intron sequence between exon 4 and exon 5B of egl-15. Comparison of protein chemical shift values for both the backbone and side chain nuclei, coupled with secondary chemical shift analysis, reveal initial details of the RNA recognition.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Anyanful A, Ono K, Johnsen RC, Ly H, Jensen V, Baillie DL, Ono S (2004) The RNA-binding protein SUP-12 controls muscle-specific splicing of the ADF/cofilin pre-mRNA in C. elegans. J Cell Biol 167:639–647
Delaglio F, Grzesiek S, Vuister GW, Zhu G, Pfeifer J, Bax A (1995) NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 6:277–293
Goodman SJ, Branda CS, Robinson MK, Burdine RD, Stern MJ (2003) Alternative splicing affecting a novel domain in the C. elegans EGL-15 FGF receptor confers functional specificity. Development 130:3757–3766
Kuroyanagi H, Kobayashi T, Mitani S, Masatoshi H (2006) Transgenic alternative-splicing reporters reveal tissue-specific expression profiles and regulation mechanisms in vivo. Nat Methods 3:909–915
Kuroyanagi H, Ohno G, Mitani S, Hagiwara M (2007) The Fox-1family and SUP-12 coordinately regulate tissue-specific alternative splicing in vivo. Mol Cell Biol 27:8612–8621
Senn H, Werner B, Messerle BA, Weber C, Traber R, Wüthrich K (1989) Stereospecific assignment of the methyl 1H NMR lines of valine and leucine in polypeptides by nonrandom 13C labelling. FEBS Lett 249:113–118
Shen Y, Delaglio F, Cornilescu G, Bax A (2009) TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts. J Biomol NMR 44:213–223
Acknowledgments
We thank Edward Sparks for assistance with cloning, as well as the Structural Biology Platform and the Analytical and Preparative Techniques Platform at the Institut Européen de Chimie et Biologie for additional assistance. This research was supported by funds from the Institut de Chimie des Substances Naturelles, the Aquitaine regional government, the Institut Européen de Chimie et Biologie, and the French national equipment network for NMR spectroscopy (TGE RMN THC Fr3050).
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Amrane, S., Mackereth, C.D. Protein chemical shift assignments of the unbound and RNA-bound forms of the alternative splicing factor SUP-12 from C. elegans . Biomol NMR Assign 8, 109–112 (2014). https://doi.org/10.1007/s12104-013-9463-9
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12104-013-9463-9