Evolutionary selection across the nuclear hormone receptor superfamily with a focus on the NR1I subfamily (vitamin D, pregnane X, and constitutive androstane receptors)

Abstract

BackgroundThe nuclear hormone receptor (NR) superfamily complement in humans is composed of 48 genes with diverse roles in metabolic homeostasis, development, and detoxification. In general, NRs are strongly conserved between vertebrate species, and few examples of molecular adaptation (positive selection) within this superfamily have been demonstrated. Previous studies utilizing two-species comparisons reveal strong purifying (negative) selection of most NR genes, with two possible exceptions being the ligand-binding domains (LBDs) of the pregnane X receptor (PXR, NR1I2) and the constitutive androstane receptor (CAR, NR1I3), two proteins involved in the regulation of toxic compound metabolism and elimination. The aim of this study was to apply detailed phylogenetic analysis using maximum likelihood methods to the entire complement of genes in the vertebrate NR superfamily. Analyses were carried out both across all vertebrates and limited to mammals and also separately for the two major domains of NRs, the DNA-binding domain (DBD) and LBD, in addition to the full-length sequences. Additional functional data is also reported for activation of PXR and the vitamin D receptor (VDR; NR1I1) to gain further insight into the evolution of the NR1I subfamily.ResultsThe NR genes appear to be subject to strong purifying selection, particularly in the DBDs. Estimates of the ratio of the non-synonymous to synonymous nucleotide substitution rates (the ω ratio) revealed that only the PXR LBD had a sub-population of codons with an estimated ω ratio greater than 1. CAR was also unusual in showing high relative ω ratios in both the DBD and LBD, a finding that may relate to the recent appearance of the CAR gene (presumably by duplication of a pre-mammalian PXR gene) just prior to the evolution of mammals. Functional analyses of the NR1I subfamily show that human and zebrafish PXRs show similar activation by steroid hormones and early bile salts, properties not shared by sea lamprey, mouse, or human VDRs, or by Xenopus laevis PXRs.ConclusionNR genes generally show strong sequence conservation and little evidence for positive selection. The main exceptions are PXR and CAR, genes that may have adapted to cross-species differences in toxic compound exposure.

Evolution and Function of the NR1I Nuclear Hormone Receptor Subfamily (VDR, PXR, and CAR) with Respect to Metabolism of Xenobiotics and Endogenous Compounds

“…Overall, the LBDs of PXR and CAR have sub-populations of codons with the highest ω ratios of any genes in the vertebrate NR superfamily [66,91]. These results strongly suggest that natural selection has favored sequence diversity in the LBD of PXR and CAR, possibly to adapt to cross-species differences in important ligands.…”

“…Not surprisingly, a study comparing human, mouse, and rat and another study comparing human, mouse, and chimpanzee revealed that genes in the NR superfamily are tightly conserved across vertebrate species and hence have likely been subjected to negative evolutionary selection [1,90]. The only two clear exceptions are the LBDs of PXR and CAR [1,66,91].…”

“…More sophisticated multi-species phylogenetic analysis utilizing maximum likelihood methods [94,97,98] reveals that sub-populations of codons within PXR genes have ω ratios exceeding one [66,91,99]. Overall, the LBDs of PXR and CAR have sub-populations of codons with the highest ω ratios of any genes in the vertebrate NR superfamily [66,91].…”

“…Relative to other PXRs such as that from zebrafish and presumably to the ancestral PXR, the BXRs have lost broad specificity for ligands, gained high efficacy activation by endogenous benzoates, and altered tissue expression pattern to play a developmental role in the frog [35,87,89]. Phylogenetic analysis by maximum likelihood shows that 23 codons in BXRα and/or BXRβ show strong evidence for positive selection [66,91]; all are in the LBD and 9 of 23 are orthologous to or adjacent to residues in human PXR shown to directly interact with ligand by x-ray crystallography [67,68,70,72]. No other PXRs show such striking features consistent with positive selection although overall phylogenetic analyses of PXR genes across species strongly suggest that the LBD of PXRs has changed across species to evolutionary advantage.…”

Structure and Function of the Human Nuclear Xenobiotic Receptor PXR

“…Krasowski and colleagues recently sug- gested that endogenous bile acids may have been the original ligands that drove PXR's evolution and species-specific variability [25]. Indeed, several groups have shown that PXR plays a crucial role in detecting the build-up of potentially toxic bile acids and up-regulating the expression of bile acid metabolizing enzymes to protect the liver and other tissues (see below).…”