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Evolution of pharmacologic specificity in the pregnane X receptor.

Ekins S, Reschly EJ, Hagey LR, Krasowski MD - BMC Evol. Biol. (2008)

Bottom Line: In addition, we compared in detail the selectivity of human and zebrafish PXRs for steroidal compounds and xenobiotics.In contrast to other nuclear hormone receptors, PXRs show significant differences in ligand specificity across species.The Western clawed frog PXR, like that described for African clawed frog PXRs, has diverged considerably in ligand selectivity from fish, bird, and mammalian PXRs.

View Article: PubMed Central - HTML - PubMed

Affiliation: Collaborations in Chemistry, Inc., Jenkintown, PA, USA. ekinssean@yahoo.com

ABSTRACT

Background: The pregnane X receptor (PXR) shows the highest degree of cross-species sequence diversity of any of the vertebrate nuclear hormone receptors. In this study, we determined the pharmacophores for activation of human, mouse, rat, rabbit, chicken, and zebrafish PXRs, using a common set of sixteen ligands. In addition, we compared in detail the selectivity of human and zebrafish PXRs for steroidal compounds and xenobiotics. The ligand activation properties of the Western clawed frog (Xenopus tropicalis) PXR and that of a putative vitamin D receptor (VDR)/PXR cloned in this study from the chordate invertebrate sea squirt (Ciona intestinalis) were also investigated.

Results: Using a common set of ligands, human, mouse, and rat PXRs share structurally similar pharmacophores consisting of hydrophobic features and widely spaced excluded volumes indicative of large binding pockets. Zebrafish PXR has the most sterically constrained pharmacophore of the PXRs analyzed, suggesting a smaller ligand-binding pocket than the other PXRs. Chicken PXR possesses a symmetrical pharmacophore with four hydrophobes, a hydrogen bond acceptor, as well as excluded volumes. Comparison of human and zebrafish PXRs for a wide range of possible activators revealed that zebrafish PXR is activated by a subset of human PXR agonists. The Ciona VDR/PXR showed low sequence identity to vertebrate VDRs and PXRs in the ligand-binding domain and was preferentially activated by planar xenobiotics including 6-formylindolo-[3,2-b]carbazole. Lastly, the Western clawed frog (Xenopus tropicalis) PXR was insensitive to vitamins and steroidal compounds and was activated only by benzoates.

Conclusion: In contrast to other nuclear hormone receptors, PXRs show significant differences in ligand specificity across species. By pharmacophore analysis, certain PXRs share similar features such as human, mouse, and rat PXRs, suggesting overlap of function and perhaps common evolutionary forces. The Western clawed frog PXR, like that described for African clawed frog PXRs, has diverged considerably in ligand selectivity from fish, bird, and mammalian PXRs.

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Conservation of ligand-binding residues. From published X-ray crystallographic structures of human VDR, rat VDR, zebrafish VDR, human PXR, human CAR, and mouse CAR (see Methods for references), amino acid residues that interact with ligands ('ligand-binding residues') were identified. At these amino acid residue positions, the sequences of Ciona intestinalis VDR/PXR, AncR1, AncR2, and AncR3 were compared with the corresponding sequence for human PXR, mouse PXR, rat PXR, rabbit PXR, chicken PXR, Xenopus laevis PXRα, Xenopus laevis PXRβ, zebrafish PXR, human CAR, human VDR, and sea lamprey VDR. The ordinate represents the percent identity of Ciona intestinalis VDR/PXR, AncR1, AncR2, and AncR3 for the corresponding sequences of PXRs, VDRs, or CAR at these ligand-binding residue positions.
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Figure 5: Conservation of ligand-binding residues. From published X-ray crystallographic structures of human VDR, rat VDR, zebrafish VDR, human PXR, human CAR, and mouse CAR (see Methods for references), amino acid residues that interact with ligands ('ligand-binding residues') were identified. At these amino acid residue positions, the sequences of Ciona intestinalis VDR/PXR, AncR1, AncR2, and AncR3 were compared with the corresponding sequence for human PXR, mouse PXR, rat PXR, rabbit PXR, chicken PXR, Xenopus laevis PXRα, Xenopus laevis PXRβ, zebrafish PXR, human CAR, human VDR, and sea lamprey VDR. The ordinate represents the percent identity of Ciona intestinalis VDR/PXR, AncR1, AncR2, and AncR3 for the corresponding sequences of PXRs, VDRs, or CAR at these ligand-binding residue positions.

Mentions: At the amino acid residue positions identified as ligand-binding residues, we compared Ciona VDR/PXR, AncR1, AncR2, and AncR3 to mammalian PXRs (human, mouse, rat, rabbit), chicken PXR, Xenopus laevis PXRα and PXRβ, zebrafish PXR, human CAR, human VDR, and sea lamprey VDR (Figure 5). As with overall sequence comparisons in the LBD (Table 5), sequence identities at ligand-binding residues for Ciona VDR/PXR compared to the other receptors were overall low (< 25%). Interestingly, AncR1 showed the highest sequence identity to human VDR (64.7%); all other sequences were less than 51% identical to AncR1 (Figure 5 and Additional file 8). This would be consistent with VDR being the ancestral NR1I receptor [51]. The differences between Ciona VDR/PXR and AncR1 at the ligand-binding residue positions may be explained by rapid evolution of the Ciona gene, as discussed above. AncR2 had the highest sequence identity at ligand-binding residues to zebrafish PXR (56.9%), compared to ~ 45–50% for other PXRs and only 31.4% to human CAR. AncR3 had highest sequence identity at ligand-binding residues to mammalian PXRs (66.7% to 70.6%) compared to only 37.3% to human CAR (Figure 5 and Additional file 8). The results for AncR2 and AncR3 both suggest that CAR has diverged the most from the ancestral sequence at ligand-binding residues and would be consistent with PXR being the ancestral gene.


Evolution of pharmacologic specificity in the pregnane X receptor.

Ekins S, Reschly EJ, Hagey LR, Krasowski MD - BMC Evol. Biol. (2008)

Conservation of ligand-binding residues. From published X-ray crystallographic structures of human VDR, rat VDR, zebrafish VDR, human PXR, human CAR, and mouse CAR (see Methods for references), amino acid residues that interact with ligands ('ligand-binding residues') were identified. At these amino acid residue positions, the sequences of Ciona intestinalis VDR/PXR, AncR1, AncR2, and AncR3 were compared with the corresponding sequence for human PXR, mouse PXR, rat PXR, rabbit PXR, chicken PXR, Xenopus laevis PXRα, Xenopus laevis PXRβ, zebrafish PXR, human CAR, human VDR, and sea lamprey VDR. The ordinate represents the percent identity of Ciona intestinalis VDR/PXR, AncR1, AncR2, and AncR3 for the corresponding sequences of PXRs, VDRs, or CAR at these ligand-binding residue positions.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
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getmorefigures.php?uid=PMC2358886&req=5

Figure 5: Conservation of ligand-binding residues. From published X-ray crystallographic structures of human VDR, rat VDR, zebrafish VDR, human PXR, human CAR, and mouse CAR (see Methods for references), amino acid residues that interact with ligands ('ligand-binding residues') were identified. At these amino acid residue positions, the sequences of Ciona intestinalis VDR/PXR, AncR1, AncR2, and AncR3 were compared with the corresponding sequence for human PXR, mouse PXR, rat PXR, rabbit PXR, chicken PXR, Xenopus laevis PXRα, Xenopus laevis PXRβ, zebrafish PXR, human CAR, human VDR, and sea lamprey VDR. The ordinate represents the percent identity of Ciona intestinalis VDR/PXR, AncR1, AncR2, and AncR3 for the corresponding sequences of PXRs, VDRs, or CAR at these ligand-binding residue positions.
Mentions: At the amino acid residue positions identified as ligand-binding residues, we compared Ciona VDR/PXR, AncR1, AncR2, and AncR3 to mammalian PXRs (human, mouse, rat, rabbit), chicken PXR, Xenopus laevis PXRα and PXRβ, zebrafish PXR, human CAR, human VDR, and sea lamprey VDR (Figure 5). As with overall sequence comparisons in the LBD (Table 5), sequence identities at ligand-binding residues for Ciona VDR/PXR compared to the other receptors were overall low (< 25%). Interestingly, AncR1 showed the highest sequence identity to human VDR (64.7%); all other sequences were less than 51% identical to AncR1 (Figure 5 and Additional file 8). This would be consistent with VDR being the ancestral NR1I receptor [51]. The differences between Ciona VDR/PXR and AncR1 at the ligand-binding residue positions may be explained by rapid evolution of the Ciona gene, as discussed above. AncR2 had the highest sequence identity at ligand-binding residues to zebrafish PXR (56.9%), compared to ~ 45–50% for other PXRs and only 31.4% to human CAR. AncR3 had highest sequence identity at ligand-binding residues to mammalian PXRs (66.7% to 70.6%) compared to only 37.3% to human CAR (Figure 5 and Additional file 8). The results for AncR2 and AncR3 both suggest that CAR has diverged the most from the ancestral sequence at ligand-binding residues and would be consistent with PXR being the ancestral gene.

Bottom Line: In addition, we compared in detail the selectivity of human and zebrafish PXRs for steroidal compounds and xenobiotics.In contrast to other nuclear hormone receptors, PXRs show significant differences in ligand specificity across species.The Western clawed frog PXR, like that described for African clawed frog PXRs, has diverged considerably in ligand selectivity from fish, bird, and mammalian PXRs.

View Article: PubMed Central - HTML - PubMed

Affiliation: Collaborations in Chemistry, Inc., Jenkintown, PA, USA. ekinssean@yahoo.com

ABSTRACT

Background: The pregnane X receptor (PXR) shows the highest degree of cross-species sequence diversity of any of the vertebrate nuclear hormone receptors. In this study, we determined the pharmacophores for activation of human, mouse, rat, rabbit, chicken, and zebrafish PXRs, using a common set of sixteen ligands. In addition, we compared in detail the selectivity of human and zebrafish PXRs for steroidal compounds and xenobiotics. The ligand activation properties of the Western clawed frog (Xenopus tropicalis) PXR and that of a putative vitamin D receptor (VDR)/PXR cloned in this study from the chordate invertebrate sea squirt (Ciona intestinalis) were also investigated.

Results: Using a common set of ligands, human, mouse, and rat PXRs share structurally similar pharmacophores consisting of hydrophobic features and widely spaced excluded volumes indicative of large binding pockets. Zebrafish PXR has the most sterically constrained pharmacophore of the PXRs analyzed, suggesting a smaller ligand-binding pocket than the other PXRs. Chicken PXR possesses a symmetrical pharmacophore with four hydrophobes, a hydrogen bond acceptor, as well as excluded volumes. Comparison of human and zebrafish PXRs for a wide range of possible activators revealed that zebrafish PXR is activated by a subset of human PXR agonists. The Ciona VDR/PXR showed low sequence identity to vertebrate VDRs and PXRs in the ligand-binding domain and was preferentially activated by planar xenobiotics including 6-formylindolo-[3,2-b]carbazole. Lastly, the Western clawed frog (Xenopus tropicalis) PXR was insensitive to vitamins and steroidal compounds and was activated only by benzoates.

Conclusion: In contrast to other nuclear hormone receptors, PXRs show significant differences in ligand specificity across species. By pharmacophore analysis, certain PXRs share similar features such as human, mouse, and rat PXRs, suggesting overlap of function and perhaps common evolutionary forces. The Western clawed frog PXR, like that described for African clawed frog PXRs, has diverged considerably in ligand selectivity from fish, bird, and mammalian PXRs.

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