Regulation of eukaryotic transcription by bHLH/PAS transcription factors AhR and Arnt.

Abstract

The Aryl hydrocarbon Receptor (AhR) is a Class I basic Helix-Loop-Helix/Per-Arnt-Sim (bHLH/PAS) transcription factor essential for adaptive response to xenobiotics. As for all bHLH/PAS proteins, it has a uniform molecular design that is composed of three functional domains, including a highly conserved N-terminal bHLH domain, a pair of degenerate PAS repeats (designated PAS.A and PAS.B), and a poorly conserved C-terminal transactivation domain. However, in contrast to the other proteins in the family, AhR is the only member known to bind xenobiotic ligand found in nature. The ligand binding domain (LBD) of AhR resides in its PAS.B region. Structure activity relationship analysis suggested that the ligand binding pocket of AhR is promiscuous, which can accommodate a large number of planar and hydrophobic compounds. Polycyclic Aromatic Hydrocarbons (PAHs) and Halogenated Aromatic Hydrocarbons (HAHs) are by far the most common classes of AhR ligands. In addition, pharmaceutical compounds such as the hepatoprotective agent YH439 that fall outside the aromatic classification, have also been shown to activate AhR, presumably by functioning as AhR agonists. To better characterize the LBD of mouse AhR (mAhR), rational site-directed mutagenesis was performed based on the LBD sequences of zebrafish (Danio rerio). Unexpectedly, the mAhR H285Y mutant as well as previously identified A375I mutant were found to discriminate between ligands, suggesting that in contrast to the PAH/HAH ligands, the atypical ligand YH439 has a novel mode of interaction that does not require full access of the ligand binding cavity. All bHLH/PAS proteins function as obligate dimers. In order to form an active, DNA binding complex, the AhR have to dimerize with Class II bHLH/PAS protein Aryl hydrocarbon receptor nuclear translocator (Arnt). This is mediated primarily via the N terminal bHLH and PAS.A domains. Furthermore, the data presented in this thesis suggest that both the α-helical connector and β-strand structure of the PAS.A domains are required for AhR/Arnt heterodimerization, which is distinct from the β-scaffold surfaces proposed for dimerization between the PAS.B domains of HIF-2α (Hypoxia Inducible Factor-2α) and Arnt. Intriguingly, interaction between Arnt and other Class I bHLH/PAS proteins were found to occur via the same dimerization interface, suggesting that the dimerization selectivity of common partner factor Arnt resides on a small number of key amino acids within a single dimerization interface of Arnt. In addition to the canonical AhR activation by xenobiotics, switching cells from adherent to suspension culture also activates the AhR, representing a non-xenobiotic, physiological activation of AhR signaling. This is further supported by the observation that AhR is recruited to the xenobiotic response element (XRE) of prototypical AhR target genes Cyp1a1, Cyp1b1 and Tiparp following both xenobiotic and suspension culture induced AhR activation. However, genome wide microarray analysis revealed significant differences between the two activation mechanisms in modulating target gene expression, implying the existence of a fine-tuning control to define the target gene specificity of AhR. Taken together, the work presented in this thesis explores the various mechanisms underlying AhR regulation with a special emphasis on specificity, which not only advances our current understanding on the non-canonical pathways of AhR activation, but also lends novel insights into how eukaryotic genes are regulated at the transcriptional level.