Structural basis of the farnesoid X receptor/retinoid X receptor heterodimer on inverted repeat DNA

Abstract

Farnesoid X receptor (FXR) is a ligand-activated transcription factor known as bile acid receptor (BAR). FXR plays critical roles in various biological processes, including metabolism, immune inflammation, liver regeneration and liver carcinogenesis. FXR forms a heterodimer with the retinoid X receptor (RXR) and binds to diverse FXR response elements (FXREs) to exert its various biological functions. However, the mechanism by which the FXR/RXR heterodimer binds the DNA elements remains unclear. In this study, we aimed to use structural, biochemical and bioinformatics analyses to study the mechanism of FXR binding to the typical FXRE, such as the IR1 site, and the heterodimer interactions in the FXR-DBD/RXR-DBD complex. Further biochemical assays showed that RAR, THR and NR4A2 do not form heterodimers with RXR when bound to the IR1 sites, which indicates that IR1 may be a unique binding site for the FXR/RXR heterodimer. Our studies may provide a further understanding of the dimerization specificity of nuclear receptors.

Keywords: Crystal structure; Farnesoid X receptor; Heterodimer; Inverted repeat DNA; Retinoid X receptor.

Graphical abstract

Fig. 1

The binding characteristic of FXR to the IR1 site. A: DNA matrix of the IR1 element. B: Occurrence of the IR1 binding motif in the FXR-binding sites. C: Binding features of FXR with IR1 in the absence of RXR or in the presence of RXR were determined by EMSA. D: DNA binding affinities of FXR and RXR to IR1 were measured by FPA.

Fig. 2

Structural analysis of the FXR-DBD/RXR-DBD/IR1 complex. A: Overall structure of the FXR-DBD/RXR-DBD/IR1 complex. The FXR-DBD and RXR-DBD molecules are colored magenta and chartreuse, respectively. The DNA is colored orange. B: DNA recognition by the FXR-DBD helix H1. C: DNA recognition by the RXR-DBD helix H1. Black dashed lines are hydrogen bonds.

Fig. 3

Protein—protein interactions in the FXR-DBD/RXR-DBD/IR1 complex. A: Surface representation of the dimerization interface in two molecules. B: Detailed stereo diagram of the residues (shown as sticks) involved in the heterodimer interface. Black dashed lines represent hydrogen bonds, red dashed lines are salt bridges. C: Binding properties of FXR variants to the IR1 site using EMSAs. D: DNA binding affinities of FXR variants to IR1 in the absence of RXR or in the presence of RXR were measured by FPA.

Fig. 4

The binding characteristic of FXR to other FXRE sites. The binding properties of FXR to other FXRE sites were measured by EMSA. The first panel is same as Fig. 1C.

Fig. 5

The binding characteristic of other nuclear receptors to the IR1 site. A: Binding properties of four nuclear receptors to the IR1 site using EMSAs. B: Occurrence of the IR1 binding motif in the RXR-binding sites. C: Structural model of the RXR/RXR homodimer on the IR1 site.

Fig. 6

Comparison with other RXR heterodimer complexes. A: RXR/RXR/DR0 (PDB code: 6XWH). B: RAR/RXR/DR1 (PDB code: 1DSZ). C: REV-ERB/REV-ERB/DR2 (PDB code: 1GA5). D: VDR/RXR/DR3 (PDB code: 1YNW). E: THR/RXR/DR4 (PDB code: 2NLL). F: RAR/RXR/DR5 (PDB code: 6XWG). G: EcR/RXR/IR1 (PDB code: 1R0N). H: GR/GR/IR3 (PDB code: 3G6P). I: NR4A2/NR4A2/IR5 (PDB code: 6L6L).