title: The Crystal Structure of the NHL Domain in Complex with RNA Reveals the Molecular Basis of Drosophila Brain-Tumor-Mediated Gene Regulation.
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.
authors.affiliation: Laboratory for RNA Biology, Biochemistry Center Regensburg, University of Regensburg, 93053 Regensburg, Germany. Electronic address: inga.loedige@embl.de.
authors.forename: Inga
authors.initials: I
authors.lastname: Loedige
authors.affiliation: Laboratory for RNA Biology, Biochemistry Center Regensburg, University of Regensburg, 93053 Regensburg, Germany.
authors.forename: Leonhard
authors.initials: L
authors.lastname: Jakob
authors.affiliation: Laboratory for RNA Biology, Biochemistry Center Regensburg, University of Regensburg, 93053 Regensburg, Germany.
authors.forename: Thomas
authors.initials: T
authors.lastname: Treiber
authors.affiliation: Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto M5S 3E1, Canada.
authors.forename: Debashish
authors.initials: D
authors.lastname: Ray
authors.affiliation: Laboratory for RNA Biology, Biochemistry Center Regensburg, University of Regensburg, 93053 Regensburg, Germany.
authors.forename: Mathias
authors.initials: M
authors.lastname: Stotz
authors.affiliation: Laboratory for RNA Biology, Biochemistry Center Regensburg, University of Regensburg, 93053 Regensburg, Germany.
authors.forename: Nora
authors.initials: N
authors.lastname: Treiber
authors.affiliation: Group Biomolecular NMR, Institute of Structural Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany.
authors.forename: Janosch
authors.initials: J
authors.lastname: Hennig
authors.affiliation: Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto M5S 3E1, Canada.
authors.forename: Kate B
authors.initials: KB
authors.lastname: Cook
authors.affiliation: Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto M5S 3E1, Canada.
authors.forename: Quaid
authors.initials: Q
authors.lastname: Morris
authors.affiliation: Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto M5S 3E1, Canada.
authors.forename: Timothy R
authors.initials: TR
authors.lastname: Hughes
authors.affiliation: Department of Statistical Bioinformatics, Institute for Functional Genomics, University of Regensburg, Josef-Engert-Straße 9, 93053 Regensburg, Germany.
authors.forename: Julia C
authors.initials: JC
authors.lastname: Engelmann
authors.affiliation: Institute for Molecular and Cellular Anatomy, University of Regensburg, 93053 Regensburg, Germany.
authors.forename: Michael P
authors.initials: MP
authors.lastname: Krahn
authors.affiliation: Laboratory for RNA Biology, Biochemistry Center Regensburg, University of Regensburg, 93053 Regensburg, Germany. Electronic address: gunter.meister@ur.de.
authors.forename: Gunter
authors.initials: G
authors.lastname: Meister
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D000818:Animals; D001665:Binding Sites; D018797:Cell Cycle Proteins / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D004330:Drosophila / Q000235:genetics / Q000378:metabolism; D029721:Drosophila Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D008969:Molecular Sequence Data; D011485:Protein Binding; D012333:RNA, Messenger / Q000378:metabolism
chemical_list: D018797:Cell Cycle Proteins; D004268:DNA-Binding Proteins; D029721:Drosophila Proteins; C107613:Mira protein, Drosophila; D012333:RNA, Messenger; C412783:brat protein, Drosophila