AHR and its Activating Molecule ARNT Heterodimer: a Transcription Factor's Response to TCDD

Jeremy Kauffman '21 and Ryan Nader '21


Contents:


I. Introduction





Functioning through the meditation of specific metabolic pathways and environmental pollutants, the ligand-activated aryl hydrocarbon receptor (AHR) is responsible for acting in a multitude of biological processes. Through multiple gene regulation pathways, AHR has been found to take part in the development of mammalian growth rate, liver function, immune system development,and female conception and lactation. AHR also plays a role in drug metabolism and detoxification of toxic combustion products such as polycyclic aromatic hydrocarbons (PAHs) and aromatic amines. AHR recognizes and binds ligands of varying nature within the cell and allows for translocation into the nucleus, where it then forms a heterodimer with the AHR nuclear translocator (ARNT) and interacts with a specific sequence of DNA, allowing for the expression of target genes.

Based on the specific ligand bound to the AHR, a variety of biological consequences may occur. More specifically, AHR has been studied extensively in regard to the recognition and binding of 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD). Once AHR binds the TCDD ligand, translocation of both AHR and the ligand into the nucleus may take place. This allows for the mediation of the TCDD carcinogen pathway. Following translocation into the nucleus, AHR forms a heterodimer with ARNT. The AHR-ARNT-TCDD complex within the nucleus binds to a genomic sequence known as the dioxin response element (DRE), expressing target genes. The expression of these genes, including genes such as cytochrome P450 1A1, cause the adverse effects associated with these highly carcinogenic dioxin pollutants. Despite our knowledge of AHR�s function specifically in regard to TCDD, other various ligand-bound AHR regulatory roles remain relatively unexplored.

II. Mechanism




After ligand-bound AHR dissociates its chaperone proteins that keep it dormant within the cytoplasm, it translocates into the nucleus to form a heterodimer with ARNT. Although, if the AHR repressor (AHRR) is present within a cell, it will bind ARNT instead and repress AHR from forming its heterodimer. This repression is done not through competition, but rather a process known as transrepression, which functions through protein-protein interactions that restrict AHR heterodimerization.

If AHRR is not present in a cell, TCDD will bind the PAS B domain of AHR and the AHR-ARNT heterodimer will form. Following the formation of the AHR-ARNT-TCDD complex, the ligand-bound heterodimer will attach to the target DNA known as the dioxin response element (DRE) and the heterodimer will act as an activator that will induce increased expression of target genes within the DRE, forming proteins such as CYP1A1. CYP1A1, which belongs to the Cytochrome p450 family of enzyme , are found in most animal cells, functioning in the metabolism of endogenous substances and the detoxification of pollutants within the organism. Although, when expression is largely upregulated with the activation of the ligand-bound transcriptional factor AHR by TCDD, these proteins catalyze harmful carcinogenic effects which include malignant tumor initiation and promotion.




III. General Structure




AHR and its activator protein ARNT both belong to the PER-ARNT-SIM (PAS)/basic helix-loop-helix (bHLH) family of transcriptional factors. The PAS domains, which are comprised of two imperfect 50 amino acid repeats known as PAS A and PAS B, are a highly conserved binding motif in which protein-protein interactions or protein signaling can occur. The PAS domain consists of a five-stranded antiparallel beta sheet and multiple alpha helices that make up the hydrophobic core, allowing both AHR and ARNT to interact with each other and ligands. The basic helix-loop-helix (bHLH) binding motif, which is found near the N-terminal region of AHR and ARNT, are binding arrangements that consist of two connected alpha helices and aid in the interactions of protein-DNA and protein-protein hetero/homodimerization. PAS-A domains aid in AHR-ARNT heterodimer formation, and the bHLH of both AHR and ARNT allow for DNA binding with the heterodimer.

The PAS B domain of AHR, also known as the ligand binding domain (LBD), specifically binds to various ligands, allowing for a conformational change in AHR. This conformational change removes the allosterically inhibiting chaperone proteins, Hsp90, P23, and ARA9 that keep AHR dormant in the cytoplasm. Once these proteins dissociate and the ligand binds, the AHR-ligand complex is able to translocate into the nucleus.

After entering the nucleus, ARNT wraps around AHR in a largely intertwined asymmetric construction. AHR-ARNT dimerization is partially governed by the largely hydrophobic points of contact to the dimerization interfaces between AHR and ARNT . The heterodimer contains up to 35 hydrophobic residues that help dimerization occur, as well as increase stability of the heterodimer and its interaction with the DRE. The bHLH domains of AHR and ARNT orient to form two similar protein extensions, one from AHR and one from ARNT, that interact with the major groove of the DRE. Sequence-specific interactions occur here as well, recognizing specifically the DRE consensus sequence T T G C G T G and differentiating it from extremely similar response elements through interactions with the bHLH protein extensions found on both the AHR and ARNT DNA binding sites. AHR-ARNT Structure Formation and It's Interaction with the DRE


IV. Recognition of and Interaction with the Dioxin Response Element




The two N-terminal bHLH protein extensions that interact with the DRE from both the AHR and ARNT are known as the alpha-1 helix arms. Both helix arm extensions are made up of positively charged amino acids that interact with the target DRE negatively charged phosphate backbone, increasing the stability of the interaction and processivity of target gene expression.

Recognition of the DRE by the AHR-ARNT heterodimer from similar response elements, such as the hypoxia response element (HRE) which differs by only one nucleotide, is crucial for allowing the proper gene expression by AHR. Arginine 39 (R39) of the AHR�s alpha-1 helix specifically aids in recognition of the proper response element by forming three hydrogen bonds with the two base moieties in the DRE: GC and CG. Arginine�s two proton donors on the NH2 residue end forms two hydrogen bonds with the guanine base oxygen and nitrogen proton acceptors. The one proton donor on the double bonded NH of the residue end forms one hydrogen bond with the guanine base oxygen proton acceptor. In the HRE, the single nucleotide difference from the DRE (G->A) allows for the absence of one of the three hydrogen bonds formed by AHR�s R39 in the DRE, allowing for the specific recognition of the DRE. Along with R39, other polar residue hydrogen bonds and salt bridge interactions on the alpha helices within the AHR-ARNT heterodimer are needed for proper DRE binding. These interactions occur within the DRE and nearby non-target DNA to efficiently bind the heterodimer to DNA, which include Arginines 38 and 39 and Lysines 62 and 65 in AHR. As well as Histidine 94, Arginines 91, 101 and 102, and Serine 91 in ARNT. It should be noted that there is an inconsistency between the PDB file and Seung-Hyeon et al. 2017 where the PDB file shows Lysine 62 binding to an Adenine, the paper shows it bound to Thymine. In addition, there should be a salt bridge interaction between Lysine 128 of the ARNT bHLH at the same point though this interaction does not seem to take place in the PDB.

V. References

Seung-Hyeon Seok, Woojong Lee, Li Jiang, Kaivalya Molugu, Aiping Zheng, Yitong Li, Sanghyun Park, Christopher A. Bradfield, and Yongna Xing. (2017). Structural hierarchy controlling dimerization and target DNA recognition in the AHR transcriptional complex. PNAS, Volume 114, Issue 21, Pages 5431-5436. https://www.pnas.org/content/114/21/5431

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Brad R. Evans, Sibel I. Karchner, Lenka L. Allan, Richard S. Pollenz, Robert L. Tanguay, Matthew J. Jenny, David H. Sherr and Mark E. Hahn. (2008). Repression of Aryl Hydrocarbon Receptor (AHR) Signaling by AHR Repressor: Role of DNA Binding and Competition for AHR Nuclear Translocator. Molecular Pharmacology, Volume 73, Issue 2, Pages 387-398. http://molpharm.aspetjournals.org/content/73/2/387

Cornelia Dietrich and Bernd Kaina. (2010). The aryl hydrocarbon receptor (AhR) in the regulation of cell�cell contact and tumor growth. Carcinogenesis, Volume 31, Issue 8, Pages 1319�1328. https://doi.org/10.1093/carcin/bgq028

Konkel, A. and Schunck, W.H. (2011). Role of cytochrome P450 enzymes in the bioactivation of polyunsaturated fatty acids. Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics, Volume 1814. Issue 1, Pages 210-222. https://www.sciencedirect.com/science/article/pii/S157096391000258X

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