Structural hierarchy controlling dimerization and target DNA recognition in the AHR transcriptional complex

Abstract

The aryl hydrocarbon receptor (AHR) belongs to the PAS (PER-ARNT-SIM) family transcription factors and mediates broad responses to numerous environmental pollutants and cellular metabolites, modulating diverse biological processes from adaptive metabolism, acute toxicity, to normal physiology of vascular and immune systems. The AHR forms a transcriptionally active heterodimer with ARNT (AHR nuclear translocator), which recognizes the dioxin response element (DRE) in the promoter of downstream genes. We determined the crystal structure of the mammalian AHR-ARNT heterodimer in complex with the DRE, in which ARNT curls around AHR into a highly intertwined asymmetric architecture, with extensive heterodimerization interfaces and AHR interdomain interactions. Specific recognition of the DRE is determined locally by the DNA-binding residues, which discriminates it from the closely related hypoxia response element (HRE), and is globally affected by the dimerization interfaces and interdomain interactions. Changes at the interdomain interactions caused either AHR constitutive nuclear localization or failure to translocate to nucleus, underlying an allosteric structural pathway for mediating ligand-induced exposure of nuclear localization signal. These observations, together with the global higher flexibility of the AHR PAS-A and its loosely packed structural elements, suggest a dynamic structural hierarchy for complex scenarios of AHR activation induced by its diverse ligands.he aryl hydrocarbon receptor (AHR) belongs to the PER-ARNT-SIM (PAS) family transcription factor that mediates broad responses to cellular and environmental cues. The AHR has been shown to be activated by diverse environmental toxicants and endogenous ligands, and play an important role in adaptive metabolism, dioxin toxicity, and normal vascular and immune development (1, 2), ever since it was identified four decades ago for mediating metabolic responses to aryl hydrocarbon toxicants (3, 4) and the acute toxicity of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) (5). The AHR was more recently found to mediate diverse cellular and physiological responses and likely respond to unknown endogenous AHR ligands (1, 2, 6-8). Developmentally, the AHR plays a role in the normal development and function of both the vascular and immune systems (9-12), and has close links to cancer, metabolic, immune, and cardiovascular diseases (13-18).Intense efforts in the past four decades have yielded important insights into the molecular processes governing AHR signaling. Newly synthesized AHR is located in cytosol and associated with the chaperones Hsp90 (19), P23 (20, 21), and AHR associated protein 9 (ARA9, also known as XAP2 or AIP) (22-24). Binding of ligands induces conformational changes in the AHR that lead to exposure of nuclear localization sequences (NLS) (25, 26). Following nuclear translocation, the AHR exchanges chaperones for a transcription partner, ARNT (1) and the AHR-ARNT heterodimer binds near the promoters of target genes at dioxin-response element (DRE...

Assembly and function of bHLH–PAS complexes

“…To explore the structural basis for this potential communication between the PAS and bHLH domains, Seok et al (1) explored the importance of interdomain interactions observed in their structure. Notably, perturbation of the bHLH-PAS-A interface in AHR appears to disconnect ligand binding from exposure of the nuclear localization signal, allowing for constitutive nuclear localization independent of ligand binding in vivo (1). This finding suggests that allosteric channels between these domains in AHR are important for ligand sensing and nuclear localization.…”

“…A careful analysis of PAS domains in CLOCK, BMAL1, NPAS1, NPAS3, ARNT, HIF1-α, and HIF2-α identified potential ligand-binding pockets in both PAS-A and PAS-B domains, suggesting the broad potential for ligand binding in these transcription factors (4). Advances in the structural biology of a native, ligand-binding bHLH-PAS complex, AHR-ARNT, by Seok et al (1) brings us one step closer to understanding native ligand binding by PAS domains and highlights the potential for discovery of ligands that similarly regulate other bHLH-PAS transcription factors.…”

“…Despite differences in their target genes and modes of regulation, these transcription factors share a common domain architecture, consisting of a bHLH DNA-binding domain followed by tandem PAS domains and intrinsically disordered C-terminal regulatory domains. In PNAS, Seok et al present the structure of the core bHLH-PAS dimer of the aryl hydrocarbon receptor (AHR)-aryl hydrocarbon nuclear receptor translocator (ARNT) transcription factor bound to DNA (1). This study provides a foundation for understanding how AHR-ARNT specifically recognizes its consensus DNA motif and highlights how changes in interdomain contacts may communicate information about ligand binding to regulate subcellular localization and transcriptional activation.…”

“…The structure of AHR-ARNT by Seok et al (1) adds to a recent bounty of bHLH-PAS structures, providing several key insights that address these fundamental questions. As the newest representative of ARNTcontaining bHLH-PAS complexes (2-4), this structure solidifies earlier observations noting a similar global architecture among heterodimers that share an ARNT subunit (Fig.…”

2,3,7,8‐Tetrachlorodibenzo‐p‐dioxin promotes injury‐induced vascular neointima formation in mice

“…TCDD-AHR complex translocates into the nucleus and binds with aryl hydrocarbon receptor nuclear translocator (ARNT). The AHR/ARNT heterodimer serves as a DNA-binding transcription factor that binds to dioxin-response elements (DREs) in the promoter region and drives the expression of target genes (16).…”