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Cell Rep. 2015 Nov 10;13(6):1206-1220. doi: 10.1016/j.celrep.2015.09.068. Epub 2015 Oct 29.

The Crystal Structure of the NHL Domain in Complex with RNA Reveals the Molecular Basis of Drosophila Brain-Tumor-Mediated Gene Regulation.

Author information

1
Laboratory for RNA Biology, Biochemistry Center Regensburg, University of Regensburg, 93053 Regensburg, Germany. Electronic address: inga.loedige@embl.de.
2
Laboratory for RNA Biology, Biochemistry Center Regensburg, University of Regensburg, 93053 Regensburg, Germany.
3
Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto M5S 3E1, Canada.
4
Group Biomolecular NMR, Institute of Structural Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany.
5
Department of Statistical Bioinformatics, Institute for Functional Genomics, University of Regensburg, Josef-Engert-Straße 9, 93053 Regensburg, Germany.
6
Institute for Molecular and Cellular Anatomy, University of Regensburg, 93053 Regensburg, Germany.
7
Laboratory for RNA Biology, Biochemistry Center Regensburg, University of Regensburg, 93053 Regensburg, Germany. Electronic address: gunter.meister@ur.de.

Abstract

TRIM-NHL proteins are conserved among metazoans and control cell fate decisions in various stem cell linages. The Drosophila TRIM-NHL protein Brain tumor (Brat) directs differentiation of neuronal stem cells by suppressing self-renewal factors. Brat is an RNA-binding protein and functions as a translational repressor. However, it is unknown which RNAs Brat regulates and how RNA-binding specificity is achieved. Using RNA immunoprecipitation and RNAcompete, we identify Brat-bound mRNAs in Drosophila embryos and define consensus binding motifs for Brat as well as a number of additional TRIM-NHL proteins, indicating that TRIM-NHL proteins are conserved, sequence-specific RNA-binding proteins. We demonstrate that Brat-mediated repression and direct RNA-binding depend on the identified motif and show that binding of the localization factor Miranda to the Brat-NHL domain inhibits Brat activity. Finally, to unravel the sequence specificity of the NHL domain, we crystallize the Brat-NHL domain in complex with RNA and present a high-resolution protein-RNA structure of this fold.

PMID:
26527002
DOI:
10.1016/j.celrep.2015.09.068
[Indexed for MEDLINE]
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