Evolution of Minimal Specificity and Promiscuity in Steroid Hormone Receptors

Abstract

Most proteins are regulated by physical interactions with other molecules; some are highly specific, but others interact with many partners. Despite much speculation, we know little about how and why specificity/promiscuity evolves in natural proteins. It is widely assumed that specific proteins evolved from more promiscuous ancient forms and that most proteins' specificity has been tuned to an optimal state by selection. Here we use ancestral protein reconstruction to trace the evolutionary history of ligand recognition in the steroid hormone receptors (SRs), a family of hormone-regulated animal transcription factors. We resurrected the deepest ancestral proteins in the SR family and characterized the structure-activity relationships by which they distinguished among ligands. We found that that the most ancient split in SR evolution involved a discrete switch from an ancient receptor for aromatized estrogens—including xenobiotics—to a derived receptor that recognized non-aromatized progestagens and corticosteroids. The family's history, viewed in relation to the evolution of their ligands, suggests that SRs evolved according to a principle of minimal specificity: at each point in time, receptors evolved ligand recognition criteria that were just specific enough to parse the set of endogenous substances to which they were exposed. By studying the atomic structures of resurrected SR proteins, we found that their promiscuity evolved because the ancestral binding cavity was larger than the primary ligand and contained excess hydrogen bonding capacity, allowing adventitious recognition of larger molecules with additional functional groups. Our findings provide an historical explanation for the sensitivity of modern SRs to natural and synthetic ligands—including endocrine-disrupting drugs and pollutants—and show that knowledge of history can contribute to ligand prediction. They suggest that SR promiscuity may reflect the limited power of selection within real biological systems to discriminate between perfect and “good enough.”

In Vitro and In Vivo Effects of Tamoxifen against Larval Stage Echinococcus granulosus

“…Furthermore, it has been proposed that during estrogen receptor evolution, specificity has been determined by the early requirement for the aromatized A ring, the final step in a conserved estrogen synthesis pathway beginning with cholesterol (37). Therein, a promiscuous ancestral SR is activated by nonsteroidal ER agonists such as DES and genistein and competitively inhibited by ER antagonists such as SERMs (37).…”

“…Therein, a promiscuous ancestral SR is activated by nonsteroidal ER agonists such as DES and genistein and competitively inhibited by ER antagonists such as SERMs (37). Tapeworms, like flukes, lack the ability to synthesize cholesterol de novo, and until now there has been no conclusive research on the biosynthesis of estrogens, progesterone, and androgens in cestodes (17).…”

Reconstructed Ancestral Enzymes Impose a Fitness Cost upon Modern Bacteria Despite Exhibiting Favourable Biochemical Properties

“…ASR uses a combination of phylogenetics, evolutionary theory, synthetic biology and protein biochemistry to infer the sequences of ancestral proteins and then characterise them in the laboratory. It has provided otherwise unobtainable insight into many evolutionary questions, such as ligand specificity in steroid hormone receptors (Bridgham et al 2006(Bridgham et al , 2009Eick et al 2012), spectral tuning in visual pigments (Chang et al 2002;Chinen et al 2005;Yokoyama et al 2008) and substrate specificity amongst fungal a-glucosidases (Voordeckers et al 2012).…”

“…To date, only a small number of ASR studies have included in vivo evaluation of inferred ancestral proteins and these have related to functionality rather than fitness (e.g. transcriptional response to different ligands [Bridgham et al 2006[Bridgham et al , 2009[Bridgham et al , 2010Eick et al 2012), ability to rescue different phenotypes (Finnigan et al 2012), ability to confer resistance to b-lactams (Risso et al 2013)]. In this study, we utilise our previously reconstructed ancestral LeuB enzymes to investigate the organismal fitness conferred by these inferred ancestral enzymes in relation to their favourable biochemical properties.…”

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

“…3 and 4 but see ref. 5). Understanding these processes is critical for a deeper understanding of molecular evolution as well as for developing therapies to target specific proteins contained within larger gene families.…”