Protein Evolution by Molecular Tinkering: Diversification of the Nuclear Receptor Superfamily from a Ligand-Dependent Ancestor
Jamie T. Bridgham1,2, Geeta N. Eick2, Claire Larroux3¤, Kirti Deshpande4, Michael J. Harms2, Marie E. A. Gauthier3, Eric A. Ortlund4, Bernard M. Degnan3, Joseph W. Thornton1,2*
1 Howard Hughes Medical Institute, Eugene, Oregon, United States of America, 2 Center for Ecology and Evolutionary Biology, University of Oregon, Eugene, Oregon, United States of America, 3 School of Biological Sciences, University of Queensland, Brisbane, Australia, 4 Biochemistry Department, Emory University School of Medicine, Atlanta, Georgia, United States of America
Abstract
Understanding how protein structures and functions have diversified is a central goal in molecular evolution. Surveys of very divergent proteins from model organisms, however, are often insufficient to determine the features of ancestral proteins and to reveal the evolutionary events that yielded extant diversity. Here we combine genomic, biochemical, functional, structural, and phylogenetic analyses to reconstruct the early evolution of nuclear receptors (NRs), a diverse superfamily of transcriptional regulators that play key roles in animal development, physiology, and reproduction. By inferring the structure and functions of the ancestral NR, we show—contrary to current belief—that NRs evolved from a ligand-activated ancestral receptor that existed near the base of the Metazoa, with fatty acids as possible ancestral ligands. Evolutionary tinkering with this ancestral structure generated the extraordinary diversity of modern receptors: sensitivity to different ligands evolved because of subtle modifications of the internal cavity, and ligand-independent activation evolved repeatedly because of various mutations that stabilized the active conformation in the absence of ligand. Our findings illustrate how a mechanistic dissection of protein evolution in a phylogenetic context can reveal the deep homology that links apparently “novel” molecular functions to a common ancestral form.
Author Summary
Many protein families are so diverse that it is hard to determine their ancestral functions and to understand how their derived functions evolved. The existence of so many different functions within protein families often creates the impression that complex, novel functions must have evolved repeatedly and independently. Nuclear receptors (NRs) are a large family of related proteins that regulate key biological processes in animals by binding to specific DNA sequences and triggering expression of nearby target genes. Many NRs are activated by a specific hormone or other small molecule, but some do not require a ligand, and still others are incapable of activating gene expression and so act primarily as repressors of transcription. To understand how the functional diversity of NRs evolved, we reconstructed the structural and functional characteristics of the ancient protein from which the entire family evolved, using genomic, biochemical, functional, and structural analyses in a phylogenetic framework. We show, contrary to current belief, that the ancestral NR was a ligand-activated transcriptional activator that existed in the earliest period of animal evolution. Our analysis reveals how the extraordinary functional diversity of modern receptors was generated by subtle tinkering with this ancestral template—slightly reshaping the ligand cavity, stabilizing the protein's active conformation so it no longer required a ligand, or disabling the protein's capacity to activate transcription without affecting its other properties. We predict that, when sufficient data are gathered to allow detailed evolutionary reconstructions in other protein families, it will become apparent that most protein functional diversity evolved by tinkering with ancient functions; invoking the evolution of wholesale “novelty” will seldom be necessary.
Citation: Bridgham JT, Eick GN, Larroux C, Deshpande K, Harms MJ, et al. (2010) Protein Evolution by Molecular Tinkering: Diversification of the Nuclear Receptor Superfamily from a Ligand-Dependent Ancestor. PLoS Biol 8(10): e1000497. doi:10.1371/journal.pbio.1000497
Academic Editor: Laurence D. Hurst, University of Bath, United Kingdom
Received: February 11, 2010; Accepted: August 17, 2010; Published: October 5, 2010
Copyright: © 2010 Bridgham et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: This work was supported by National Science Foundation grant IOB-0546906 (JWT) and National Institutes of Health grants R01-GM081592 (JWT), F32-GM074398 (JTB), and F32-GM090650 (MJH). JWT is an Early Career Scientist of the Howard Hughes Medical Institute. BMD is supported by the Australian Research Council. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist.
Abbreviations: AncNR, ancestral NR; CAR, constitutive androstane receptor; DBD, DNA-binding domain; FA, fatty acid; LBD, ligand-binding domain
* E-mail: joet@uoregon.edu
¤ Current address: Department of Earth & Environmental Sciences, Ludwig-Maximilians-University, Munich, Germany
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