MBE Advance Access published online on January 6, 2009
Molecular Biology and Evolution, doi:10.1093/molbev/msn302
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Research Article |
Structural and Evolutionary Innovation of the Heterodimerisation Interface between USP and the Ecdysone Receptor ECR in Insects
1 IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), Département de Biologie et de Génomique Structurales, Illkirch, F-67400 France; INSERM, U596, Illkirch, F-67400 France; CNRS, UMR7104, Illkirch, F-67400 France; Université Louis Pasteur, Faculté des Sciences de la Vie, Strasbourg, F-67000 France
2 Institut de Génomique fonctionnelle de Lyon; Université de Lyon; Université Lyon 1, CNRS, INRA, ENS de Lyon, France
3 Cemagref, UR BELY, F-69336 Lyon, France
4 Department of Ecology and Evolution, Université de Lausanne, CH-1015 Lausanne, Switzerland
5 Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
6 Present address: IBS (Institut de Biologie Structurale), LCCP, 41, rue Jules Horowitz; 38027 Grenoble Cedex 1, France
Corresponding Author: Thomas Iwema, Institut de Biologie Structurale (IBS), LCCP., 41 rue Jules Horowitz, 38027 GRENOBLE Cedex 1, France, Tel: +33 (0)4 38 78 95 96, Fax: +33 (0)4 38 78 51 22, E-mail: thomas.iwema{at}ibs.fr and thomas.iwema{at}gmail.com
Received for publication October 6, 2008. Revision received December 22, 2008. Accepted for publication December 23, 2008.
Understanding how the variability of protein structure arises during evolution and leads to new structure-function relationships ultimately promoting evolutionary novelties is a major goal of molecular evolution and is critical for interpreting genome sequences. We addressed this issue using the ecdysone receptor, a major developmental factor which controls development and reproduction of arthropods. The functional ecdysone receptor is a heterodimer of two nuclear receptors: ECR, which binds ecdysteroids, and its obligatory partner USP which is orthologous to the retinoid X receptor (RXR) of vertebrates. Both genes underwent a dramatic increase of evolutionary rate in Mecopterida, the major insect terminal group containing Dipteras and Lepidopteras. We therefore questioned the implication of this event in terms of coevolution of their dimerisation interface.
A structural comparison revealed a 30% larger Ligand Binding Domain (LBD) heterodimerisation surface in the Lepidoptera Heliothis when compared to basal insects, associated with a symmetrisation of the interface which is exceptional for nuclear receptors. Reconstruction of ancestral sequences and homology modelling of the ancestral Mecopterida ECR-USP reveal that this enlarged dimerisation surface is a synapomorphy for Mecopterida. Furthermore, we show that the residues implicated in the new dimerisation surface underwent specific evolutionary constraints in Mecopterida indicative of their new and conserved role in the dimerisation interface. Most of all, the novel surface originates from a 15° torsion of a subdomain of USP LBD toward its partner ECR which is a long range consequence of the peculiar position of a Mecopterida specific insertion in loop L1-3, located outside of the interaction surface, in a less crucial domain of the partner protein. These results indicate that the coevolution between ECR and USP occurred through a novel mechanism of intra-molecular epistasis which will undoubtedly be generalised for other molecules since it uses flexibility of a less constrained region of a protein to modify the structure of another, critical part of the molecule.
Key Words: nuclear receptors, heterodimerisation, 3D structure • Mecopterida, epistasis
7 These authors contributes equally to this work