Reverse yeast two-hybrid system to identify mammalian nuclear receptor residues that interact with ligands and/or antagonists.

Abstract

As a critical regulator of drug metabolism and inflammation, Pregnane X Receptor (PXR), plays an important role in disease pathophysiology linking metabolism and inflammation (e.g. hepatic steatosis)(1,2). There has been much progress in the identification of agonist ligands for PXR, however, there are limited descriptions of drug-like antagonists and their binding sites on PXR(3,4,5). A critical barrier has been the inability to efficiently purify full-length protein for structural studies with antagonists despite the fact that PXR was cloned and characterized in 1998. Our laboratory developed a novel high throughput yeast based two-hybrid assay to define an antagonist, ketoconazole's, binding residues on PXR(6). Our method involves creating mutational libraries that would rescue the effect of single mutations on the AF-2 surface of PXR expected to interact with ketoconazole. Rescue or "gain-of-function" second mutations can be made such that conclusions regarding the genetic interaction of ketoconazole and the surface residue(s) on PXR are feasible. Thus, we developed a high throughput two-hybrid yeast screen of PXR mutants interacting with its coactivator, SRC-1. Using this approach, in which the yeast was modified to accommodate the study of the antifungal drug, ketoconazole, we could demonstrate specific mutations on PXR enriched in clones unable to bind to ketoconazole. By reverse logic, we conclude that the original residues are direct interaction residues with ketoconazole. This assay represents a novel, tractable genetic assay to screen for antagonist binding sites on nuclear receptor surfaces. This assay could be applied to any drug regardless of its cytotoxic potential to yeast as well as to cellular protein(s) that cannot be studied using standard structural biology or proteomic based methods. Potential pitfalls include interpretation of data (complementary methods useful), reliance on single Y2H method, expertise in handling yeast or performing yeast two-hybrid assays, and assay optimization.

• Authors: Hao Li, Wei Dou, Emil Padikkala, Sridhar Mani
• Journal: Journal of visualized experiments : JoVE (J Vis Exp) Issue 81 Pg. e51085 (Nov 15 2013) ISSN: 1940-087X [Electronic] United States
• PMID: 24300333 (Publication Type: Journal Article, Research Support, N.I.H., Extramural, Research Support, Non-U.S. Gov't, Video-Audio Media)

Chemical References

• DNA-Binding Proteins
• GAL4 protein, S cerevisiae
• Ligands
• Pregnane X Receptor
• Receptors, Steroid
• Recombinant Fusion Proteins
• Saccharomyces cerevisiae Proteins
• Transcription Factors
• NCOA1 protein, human
• Nuclear Receptor Coactivator 1
• Ketoconazole

Topics

• Binding Sites
• DNA-Binding Proteins (genetics, metabolism)
• Humans
• Ketoconazole (pharmacology)
• Ligands
• Nuclear Receptor Coactivator 1 (genetics, metabolism)
• Pregnane X Receptor
• Receptors, Steroid (antagonists & inhibitors, genetics, metabolism)
• Recombinant Fusion Proteins (genetics, metabolism)
• Saccharomyces cerevisiae (genetics, metabolism)
• Saccharomyces cerevisiae Proteins (genetics, metabolism)
• Transcription Factors (genetics, metabolism)
• Two-Hybrid System Techniques