Dimerization of doublesex is mediated by a cryptic ubiquitin-associated domain fold - Implications for sex-specific gene regulation
ABSTRACT Male- and female-specific isoforms of the Doublesex (DSX) transcription factor regulate somatic sexual differentiation in Drosophila. The isoforms (DSX(M) and DSX(F)) share an N-terminal DNA binding domain (the DM motif), broadly conserved among metazoan sex-determining pathways. DM-DNA recognition is enhanced by a C-terminal dimerization domain. The crystal structure of this domain, determined at a resolution of 1.6 A, reveals a novel dimeric arrangement of ubiquitin-associated (UBA) folds. Although this alpha-helical motif is well characterized in pathways of DNA repair and subcellular trafficking, to our knowledge this is its first report in a transcription factor. Dimerization is mediated by a non-canonical hydrophobic interface extrinsic to the putative ubiquitin binding surface. Key side chains at this interface, identified by alanine scanning mutagenesis, are conserved among DSX homologs. The mechanism of dimerization is thus unrelated to the low affinity domain swapping observed among ubiquitin-associated CUE domains. The unexpected observation of a ubiquitin-associated fold in DSX extends the repertoire of alpha-helical dimerization elements in transcription factors. The possibility that the ubiquitination machinery participates in the regulation of sexual dimorphism is discussed.
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ABSTRACT: Primary sex-determination ''switches'' evolve ra-pidly, but Doublesex (DSX)-related transcription fac-tors (DMRTs) act downstream of these switches to control sexual development in most animal species. Drosophila dsx encodes female-and male-specific isoforms (DSX F and DSX M), but little is known about how dsx controls sexual development, whether DSX F and DSX M bind different targets, or how DSX proteins direct different outcomes in diverse tissues. We undertook genome-wide analyses to identify DSX targets using in vivo occupancy, binding site predic-tion, and evolutionary conservation. We find that DSX F and DSX M bind thousands of the same targets in multiple tissues in both sexes, yet these targets have sex-and tissue-specific functions. Interestingly, DSX targets show considerable overlap with targets identified for mouse DMRT1. DSX targets include transcription factors and signaling pathway compo-nents providing for direct and indirect regulation of sex-biased expression. INTRODUCTIONDevelopmental Cell 12/2014; 31(6):761-773. DOI:10.1016/j.devcel.2014.11.021 · 10.37 Impact Factor
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ABSTRACT: Although residue-residue contact maps dictate the topology of proteins, sequence-based ab initio contact predictions have been found little use in actual structure prediction due to the low accuracy. We developed a composite set of nine SVM-based contact predictors that are used in I-TASSER simulation in combination with sparse template contact restraints. When testing the strategy on 273 nonhomologous targets, remarkable improvements of I-TASSER models were observed for both easy and hard targets, with p value by Student's t test<0.00001 and 0.001, respectively. In several cases, template modeling score increases by >30%, which essentially converts "nonfoldable" targets into "foldable" ones. In CASP9, I-TASSER employed ab initio contact predictions, and generated models for 26 FM targets with a GDT-score 16% and 44% higher than the second and third best servers from other groups, respectively. These findings demonstrate a new avenue to improve the accuracy of protein structure prediction especially for free-modeling targets.Structure 08/2011; 19(8):1182-91. DOI:10.1016/j.str.2011.05.004 · 6.79 Impact Factor
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ABSTRACT: The doublesex (dsx) gene of the parasitic wasp Nasonia vitripennis is described and characterized. Differential splicing of dsx transcripts has been shown to induce somatic sexual differentiation in Diptera and Lepidoptera, but not yet in other insect orders. Two spliceforms of Nasonia dsx mRNA are differentially expressed in males and females. In addition, in a gynandromorphic line that produces haploids (normally males) with full female phenotypes, these individuals show the female spliceform, providing the first demonstration of a direct association of dsx with somatic sex differentiation in Hymenoptera. Finally, the DNA binding (DM) domain of Nasonia dsx clusters phylogenetically with dsx from other insects, and Nasonia dsx shows microsynteny with dsx of Apis, further supporting identification of the dsx orthologue in Nasonia.Insect Molecular Biology 07/2009; 18(3):315-24. DOI:10.1111/j.1365-2583.2009.00874.x · 2.98 Impact Factor