TAR DNA-binding protein 43 (TDP-43) is a ubiquitously expressed nuclear protein that influences diverse cellular processes by regulating alternative splicing of RNA and microRNA biogenesis. It is also a pathological protein found in sporadic ALS and in the most common subtype of frontotemporal lobar degeneration with ubiquitinated inclusions (FLTD-U). TDP-43 has two tandem RNA-binding domains, RRM1 and RRM2. The NMR structure of TDP-43 was solved in the presence of UG-rich RNA sequences bound to the RRM1 and RRM2 domains. Here we report the backbone assignment of apo TDP-43. The chemical shift (HN, N, C, Cα and Cβ) analysis shows the predicted regions of secondary structure are in good agreement with those observed for TDP-43 in complex with RNA. However, our data show that the apo structure of TPD-43 has increased flexibility in the regions that would normally have been used to anchor the RNA bases. The backbone chemical shifts assignments will prove useful in the study of TDP-43 interaction with non-canonical RNA and RRM-binding proteins.
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We thank Dr. Michael Clarkson, Staff Scientist at the University of Arizona, and Dr. Brian Cherry, Associate Research Professional at Arizona State University Magnetic Resonance Research Center for their help with NMR acquisition. This work was supported by grants from 2014 AHSC-CDA Arizona Health Sciences Career Development Award, and AZ ABRC ADHS16-162407 Arizona Grant.
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Scott, D.D., Francois-Moutal, L., Kumirov, V.K. et al. 1H, 15N and 13C backbone assignment of apo TDP-43 RNA recognition motifs. Biomol NMR Assign 13, 163–167 (2019). https://doi.org/10.1007/s12104-018-09870-x
- RNA recognition motif
- Chemical shift assignment
- Secondary structure