Hudson William H, Kossmann Bradley R, de Vera Ian Mitchelle S, Chuo Shih-Wei, Weikum Emily R, Eick Geeta N, Thornton Joseph W, Ivanov Ivaylo N, Kojetin Douglas J, Ortlund Eric A
Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322;
Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30302;
Proc Natl Acad Sci U S A. 2016 Jan 12;113(2):326-31. doi: 10.1073/pnas.1518960113. Epub 2015 Dec 29.
Many genomes contain families of paralogs--proteins with divergent function that evolved from a common ancestral gene after a duplication event. To understand how paralogous transcription factors evolve divergent DNA specificities, we examined how the glucocorticoid receptor and its paralogs evolved to bind activating response elements [(+)GREs] and negative glucocorticoid response elements (nGREs). We show that binding to nGREs is a property of the glucocorticoid receptor (GR) DNA-binding domain (DBD) not shared by other members of the steroid receptor family. Using phylogenetic, structural, biochemical, and molecular dynamics techniques, we show that the ancestral DBD from which GR and its paralogs evolved was capable of binding both nGRE and (+)GRE sequences because of the ancestral DBD's ability to assume multiple DNA-bound conformations. Subsequent amino acid substitutions in duplicated daughter genes selectively restricted protein conformational space, causing this dual DNA-binding specificity to be selectively enhanced in the GR lineage and lost in all others. Key substitutions that determined the receptors' response element-binding specificity were far from the proteins' DNA-binding interface and interacted epistatically to change the DBD's function through DNA-induced allosteric mechanisms. These amino acid substitutions subdivided both the conformational and functional space of the ancestral DBD among the present-day receptors, allowing a paralogous family of transcription factors to control disparate transcriptional programs despite high sequence identity.
许多基因组包含旁系同源基因家族——这些蛋白质功能不同，在一次复制事件后从一个共同的祖先基因进化而来。为了了解旁系同源转录因子如何进化出不同的DNA特异性，我们研究了糖皮质激素受体及其旁系同源基因如何进化以结合激活反应元件[（+）GREs]和负糖皮质激素反应元件（nGREs）。我们发现，与nGREs结合是糖皮质激素受体（GR）DNA结合结构域（DBD）的特性，类固醇受体家族的其他成员并不具备这一特性。利用系统发育、结构、生化和分子动力学技术，我们发现GR及其旁系同源基因进化而来的祖先DBD能够结合nGRE和（+）GRE序列，这是因为祖先DBD能够呈现多种DNA结合构象。随后，复制的子代基因中的氨基酸取代选择性地限制了蛋白质的构象空间，导致这种双重DNA结合特异性在GR谱系中被选择性增强，而在所有其他谱系中丧失。决定受体反应元件结合特异性的关键取代远离蛋白质的DNA结合界面，并通过DNA诱导的变构机制进行上位性相互作用以改变DBD的功能。这些氨基酸取代在当今的受体之间划分了祖先DBD的构象和功能空间，使得旁系同源转录因子家族能够控制不同的转录程序，尽管它们的序列同一性很高。
