Distal substitutions drive divergent DNA specificity among paralogous transcription factors through subdivision of conformational space

• Type of Material: Article
• Authors: William Hudson, Emory University; Bradley R. Kossmann, Georgia State University; Ian Mitchelle S. de Vera, Scripps Florida; Shih-Wei Chuo, Georgia State University; Emily R. Weikum, Emory University; Geeta N. Eick, University of Oregon; Joseph W. Thornton, University of Chicago; Ivaylo N. Ivanov, Georgia State University; Douglas J. Kojetin, Scripps Florida; Eric Ortlund, Emory University
• Language: English
• Date: 2016-01-12
• Publisher: NATL ACAD SCIENCES
• Publication Version: Final Published Version
• Copyright Statement: National Academy of Sciences
• Final Published Version (URL): http://dx.doi.org/10.1073/pnas.1518960113
• Title of Journal or Parent Work: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• Volume: 113
• Issue: 2
• Start Page: 326
• End Page: 331
• Grant/Funding Information: E.A.O. is supported by NIH Grant R01DK095750, AHA Grant 14GRNT20460124, and a W. M. Keck Foundation Medical Research Grant.; W.H.H. is supported by Emory–National Institute of Health (NIH) Pharmacological Sciences Graduate Training Grant 5T32GM008602 and by American Heart Association (AHA) Predoctoral Fellowship 13PRE16920012.; I.N.I. is supported by National Science Foundation (NSF) CAREER Award MCB-1149521 and NIH Grant R01GM110387.; Computational resources were provided in part by an NSF XSEDE allocation, CHE110042, and through an allocation at the National Energy Research Scientific Computing Center (NERSC) supported by US Department of Energy (DOE) Office of Science Contract DE-AC02-05CH11231.; D.J.K. is supported by NIH Grants R01DK101871 and R01GM114420.; J.W.T. is supported by NIH Grant 5R01GM104397.; Use of the Advanced Photon Source was supported by the DOE Contract W-31-109-Eng-38.; B.R.K. is supported by a Molecular Basis of Disease fellowship at Georgia State University.
• Keywords: TRANSREPRESSION; Science & Technology - Other Topics; C-JUN; ANCIENT PROTEIN; glucocorticoid; DIRECTED EVOLUTION; EPISTASIS; evolution; Multidisciplinary Sciences; steroid receptors; epistasis; MUTATIONS; STEROID-HORMONE RECEPTORS; BINDING DOMAIN; Science & Technology; NF-KAPPA-B; GLUCOCORTICOID-RECEPTOR EVOLUTION
• Research Categories: Biology, Ecology; Chemistry, Biochemistry; Biology, Genetics

Abstract

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 elementbinding 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.