Aryl hydrocarbon receptor (AHR): "pioneer member" of the basic-helix/loop/helix per-Arnt-sim (bHLH/PAS) family of "sensors" of foreign and endogenous signals

Abstract

The basic-helix/loop/helix per-Arnt-sim (bHLH/PAS) family comprises many transcription factors, found throughout all three kingdoms of life; bHLH/PAS members "sense" innumerable intracellular and extracellular "signals" - including endogenous compounds, foreign chemicals, gas molecules, redox potential, photons (light), gravity, heat, and osmotic pressure. These signals then initiate downstream signaling pathways involved in responding to that signal. The term "PAS", abbreviation for "per-Arnt-sim" was first coined in 1991. Although the mouse Arnt gene was not identified until 1991, evidence of its co-transcriptional binding partner, aryl hydrocarbon receptor (AHR), was first reported in 1974 as a "sensor" of foreign chemicals, up-regulating cytochrome P450 family 1 (CYP1) and other enzyme activities that usually metabolize the signaling chemical. Within a few years, AHR was proposed also to participate in inflammation. The mouse [Ah] locus was shown (1973-1989) to be relevant to chemical carcinogenesis, mutagenesis, toxicity and teratogenesis, the mouse Ahr gene was cloned in 1992, and the first Ahr(-/-) knockout mouse line was reported in 1995. After thousands of studies from the early 1970s to present day, we now realize that AHR participates in dozens of signaling pathways involved in critical-life processes, affecting virtually every organ and cell-type in the animal, including many invertebrates.

Keywords: AHR; Cancer; Dose-response curve; Eicosanoids; Embryonic stem cells; Lipid mediators; Mouse genetics; Pro-inflammatory and post-inflammatory response; Prostaglandins; bHLH/PAS family of transcription factors; “Brain-gut-microbiome”.

Fig. 1

Dose-response curve of induced AHH activity (the CYP1A1 monooxygenase), as a function of intraperitoneal TCDD administered 48 h earlier — comparing B6 (C57BL/6 mouse with high-affinity AHR) with D2 (DBA/2 mouse with poor-affinity AHR). Units on Y-axis denote “nmol of 3-hydroxybenzo[a]pyrene formed per min per mg liver microsomal protein” [redrawn and modified from data in (Poland et al., 1974)].

Fig. 2

Schematic representation of bHLH/PAS sensor proteins, in which specific functions are localized to particular regions, or modules. Ligands bind to the PAS-B domain; binding to HSP90 includes both the bHLH and PAS-B domains; dimerization with ARNT involves both the bHLH domain and PAS domains; DNA-binding and the nuclear localization signal reside in the basic region of the bHLH domain; the trans-activation function comprises a large segment toward the carboxy (COOH)-terminus. The carboxyl half of AHR protein displays the greatest amino-acid variation across the animal kingdom, whereas bHLH/PAS domains are highly conserved [redrawn and modified from (Okey, 2007) and references therein].

Fig. 3

LM second-messenger pathways, derived from (ω–6)- and (ω–3)-fatty acids. The former gives rise to eleven classes of LMs derived from arachidonic acid (AA). The latter gives rise to four classes of LMs derived from eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA). Enzymes involved in the synthesis and degradation of the more than 150 total LMs in the 15 classes include two cyclooxygenases, members from six families of CYP monooxygenases, plus arachidonate lipooxygenases (ALOXs; six in human; seven in mouse). The “active” LMs are then “sensed by” (bind to) appropriate receptors in various organs and cell types, leading downstream to virtually every critical-life response in the organism [modified from (Nebert et al., 2013b)].

Fig. 4

Polyunsaturated fatty acids (PUFAs), lipoxygenase vs monooxygenase mechanisms of reactions, and LM biosynthesis pathways. A, scheme depicting the origin of ω–6 and ω–3 LMs. B, diagram showing mechanism for the lipoxygenase reaction. C, diagram showing mechanisms for the P450-monooxygenase reactions.

Fig. 4

Polyunsaturated fatty acids (PUFAs), lipoxygenase vs monooxygenase mechanisms of reactions, and LM biosynthesis pathways. A, scheme depicting the origin of ω–6 and ω–3 LMs. B, diagram showing mechanism for the lipoxygenase reaction. C, diagram showing mechanisms for the P450-monooxygenase reactions.

Fig. 4

Polyunsaturated fatty acids (PUFAs), lipoxygenase vs monooxygenase mechanisms of reactions, and LM biosynthesis pathways. A, scheme depicting the origin of ω–6 and ω–3 LMs. B, diagram showing mechanism for the lipoxygenase reaction. C, diagram showing mechanisms for the P450-monooxygenase reactions.

Fig. 4

Polyunsaturated fatty acids (PUFAs), lipoxygenase vs monooxygenase mechanisms of reactions, and LM biosynthesis pathways. A, scheme depicting the origin of ω–6 and ω–3 LMs. B, diagram showing mechanism for the lipoxygenase reaction. C, diagram showing mechanisms for the P450-monooxygenase reactions.

Fig. 5

LM metabolites that were able to be identified and quantified by the multiple-reaction monitoring and liquid chromatography-UV coupled with tandem mass spectrometry-based LM metabololipidomics system used (Divanovic et al., 2013). The three LM metabolomes include: A, arachidonic acid (AA)-derived, B, docosahexaenoic acid (DHA)-derived, and C, eicosapentaenoic acid (EPA)-derived LMs. For various metabolites in the pathways, some of the established critical-life processes elicited by specific LMs are depicted in the rectangular boxes. Processes described in red font denote pro-inflammatory and pro-resolving inflammatory functions, i.e. initiation and resolution of inflammation, respectively.

Fig. 5

LM metabolites that were able to be identified and quantified by the multiple-reaction monitoring and liquid chromatography-UV coupled with tandem mass spectrometry-based LM metabololipidomics system used (Divanovic et al., 2013). The three LM metabolomes include: A, arachidonic acid (AA)-derived, B, docosahexaenoic acid (DHA)-derived, and C, eicosapentaenoic acid (EPA)-derived LMs. For various metabolites in the pathways, some of the established critical-life processes elicited by specific LMs are depicted in the rectangular boxes. Processes described in red font denote pro-inflammatory and pro-resolving inflammatory functions, i.e. initiation and resolution of inflammation, respectively.

Fig. 5

LM metabolites that were able to be identified and quantified by the multiple-reaction monitoring and liquid chromatography-UV coupled with tandem mass spectrometry-based LM metabololipidomics system used (Divanovic et al., 2013). The three LM metabolomes include: A, arachidonic acid (AA)-derived, B, docosahexaenoic acid (DHA)-derived, and C, eicosapentaenoic acid (EPA)-derived LMs. For various metabolites in the pathways, some of the established critical-life processes elicited by specific LMs are depicted in the rectangular boxes. Processes described in red font denote pro-inflammatory and pro-resolving inflammatory functions, i.e. initiation and resolution of inflammation, respectively.

Fig. 5

LM metabolites that were able to be identified and quantified by the multiple-reaction monitoring and liquid chromatography-UV coupled with tandem mass spectrometry-based LM metabololipidomics system used (Divanovic et al., 2013). The three LM metabolomes include: A, arachidonic acid (AA)-derived, B, docosahexaenoic acid (DHA)-derived, and C, eicosapentaenoic acid (EPA)-derived LMs. For various metabolites in the pathways, some of the established critical-life processes elicited by specific LMs are depicted in the rectangular boxes. Processes described in red font denote pro-inflammatory and pro-resolving inflammatory functions, i.e. initiation and resolution of inflammation, respectively.

Fig. 6

Hypothesis designed for the study of peritoneal exudate of zymosan-treated mice (Divanovic et al., 2013). A, B and C denote metabolites in the LM second-messenger cascade that can be identified and quantified by the multiple-reaction monitoring and liquid chromatography-UV coupled with tandem mass spectrometry-based LM metabololipidomics system (Divanovic et al., 2013). If CYP1A1, CYP1A2 and CYP1B1 monooxygenases are all involved, just two involved, or just one of the three enzymes involved — in a metabolic step between A and B, then metabolite B levels will be decreased in TKO mice, compared with wild-type (WT) mice. If three, two or one of the CYP1 enzymes are(is) involved in a metabolic step between B and C, then metabolite B levels will be increased in TKO mice, compared with WT mice.

Fig. 6

Hypothesis designed for the study of peritoneal exudate of zymosan-treated mice (Divanovic et al., 2013). A, B and C denote metabolites in the LM second-messenger cascade that can be identified and quantified by the multiple-reaction monitoring and liquid chromatography-UV coupled with tandem mass spectrometry-based LM metabololipidomics system (Divanovic et al., 2013). If CYP1A1, CYP1A2 and CYP1B1 monooxygenases are all involved, just two involved, or just one of the three enzymes involved — in a metabolic step between A and B, then metabolite B levels will be decreased in TKO mice, compared with wild-type (WT) mice. If three, two or one of the CYP1 enzymes are(is) involved in a metabolic step between B and C, then metabolite B levels will be increased in TKO mice, compared with WT mice.

Fig. 6

Hypothesis designed for the study of peritoneal exudate of zymosan-treated mice (Divanovic et al., 2013). A, B and C denote metabolites in the LM second-messenger cascade that can be identified and quantified by the multiple-reaction monitoring and liquid chromatography-UV coupled with tandem mass spectrometry-based LM metabololipidomics system (Divanovic et al., 2013). If CYP1A1, CYP1A2 and CYP1B1 monooxygenases are all involved, just two involved, or just one of the three enzymes involved — in a metabolic step between A and B, then metabolite B levels will be decreased in TKO mice, compared with wild-type (WT) mice. If three, two or one of the CYP1 enzymes are(is) involved in a metabolic step between B and C, then metabolite B levels will be increased in TKO mice, compared with WT mice.

Fig. 6

Hypothesis designed for the study of peritoneal exudate of zymosan-treated mice (Divanovic et al., 2013). A, B and C denote metabolites in the LM second-messenger cascade that can be identified and quantified by the multiple-reaction monitoring and liquid chromatography-UV coupled with tandem mass spectrometry-based LM metabololipidomics system (Divanovic et al., 2013). If CYP1A1, CYP1A2 and CYP1B1 monooxygenases are all involved, just two involved, or just one of the three enzymes involved — in a metabolic step between A and B, then metabolite B levels will be decreased in TKO mice, compared with wild-type (WT) mice. If three, two or one of the CYP1 enzymes are(is) involved in a metabolic step between B and C, then metabolite B levels will be increased in TKO mice, compared with WT mice.

Fig 7

Identification of metabolic steps at which CYP1 enzymes are proposed to participate (Divanovic et al., 2013). A, AA-derived lipoxins, prostaglandins, thromboxanes, and leukotrienes. B, DHA-derived resolvins, protectins and maresins. C, EPA-derived resolvins. CYP1 labels are placed in accordance with the findings in the study, combined with what is known about CYP-mediated LM metabolism: “way up” or “way down” = P <0.05; “up” or “down” = P <0.08 > 0.05; and * denotes “Trend,” = P <0.12 > 0.08. Positions of the (bolded red) CYP1 labels and the bolded red asterisks depict the proposed steps, as determined in the study (Divanovic et al., 2013). In cases where there are two or more steps between the identifiable LM metabolite, the precise step at which CYP1 acts, and which one (or two or three) of the three CYP1 enzymes participates — will require further experiments.

Fig 7

Identification of metabolic steps at which CYP1 enzymes are proposed to participate (Divanovic et al., 2013). A, AA-derived lipoxins, prostaglandins, thromboxanes, and leukotrienes. B, DHA-derived resolvins, protectins and maresins. C, EPA-derived resolvins. CYP1 labels are placed in accordance with the findings in the study, combined with what is known about CYP-mediated LM metabolism: “way up” or “way down” = P <0.05; “up” or “down” = P <0.08 > 0.05; and * denotes “Trend,” = P <0.12 > 0.08. Positions of the (bolded red) CYP1 labels and the bolded red asterisks depict the proposed steps, as determined in the study (Divanovic et al., 2013). In cases where there are two or more steps between the identifiable LM metabolite, the precise step at which CYP1 acts, and which one (or two or three) of the three CYP1 enzymes participates — will require further experiments.

Fig 7

Identification of metabolic steps at which CYP1 enzymes are proposed to participate (Divanovic et al., 2013). A, AA-derived lipoxins, prostaglandins, thromboxanes, and leukotrienes. B, DHA-derived resolvins, protectins and maresins. C, EPA-derived resolvins. CYP1 labels are placed in accordance with the findings in the study, combined with what is known about CYP-mediated LM metabolism: “way up” or “way down” = P <0.05; “up” or “down” = P <0.08 > 0.05; and * denotes “Trend,” = P <0.12 > 0.08. Positions of the (bolded red) CYP1 labels and the bolded red asterisks depict the proposed steps, as determined in the study (Divanovic et al., 2013). In cases where there are two or more steps between the identifiable LM metabolite, the precise step at which CYP1 acts, and which one (or two or three) of the three CYP1 enzymes participates — will require further experiments.

Fig. 8

Established effects of AHR and the AHR-CYP1 axis on cell cycle functions. Arrows denote “activation or stimulation” whereas lines with a foot indicate “repression or inhibition.” A, blue circle denotes the cell cycle (G₁ –> S –> G₂ –> M –> return to the G₁ phase). The G₁/S cell cycle checkpoint controls commitment of eukaryotic cells to transition through the G₁ phase to enter into the DNA synthesis S phase. The G₂/M checkpoint precedes the cell’s entrance into mitosis, with locations indicated when cells have specific options (e.g. G₀ for the inactive, or resting, phase; versus processes such as apoptosis, differentiation, and proliferation). Two cell cycle kinase complexes — CDK4/6 (cyclin-dependent kinase 4 & 6)-CCND1 (cyclin D1), and CDK2-CCNE1 (cyclin E1) — participate as part of a dynamic transcription complex, to move the cell from G₁ to S phase (described further in panel 8B). DNA damage (upper right) activates ATM and ATR (serine-threonine kinases), and also represses MDM2 and MDM4 (MDM proto-oncogenes 2 & 4), thereby releasing their inhibition of TP53 in concert with activation of TP53 by ATM/ATR. Phosphorylation (P denotes inorganic PO₄) of TP53 by PP2A (protein phosphatase-2A), via several steps, activates PAK1–6 (p21 (RAC1; CDKN1A)-activated kinases-1 through -6), which results in repression of CDK2. Whereas CDC25A (cell division cycle-25A) activates both CDK4/6 and CDK2, CDC25A is suppressed by CHEK1/2. At the M/G₁ boundary (lower left), the CDC25B/26-CDK1 complex induces either differentiation or proliferation. Activated AHR* stimulates the complex of POU5F1 (POU class-5 homeobox-1; formerly OCT4) and SOX2 (SRY-box-2), which in turn up-regulates MID1 (midline-1), thus allowing MID1 to activate mitosis. For the sake of avoiding clutter, many additional factors participating in the cell cycle are not shown. The two cell cycle kinase complexes — CDK4/6-CCND1 (cyclin D1) and CDK2-CCNE1 (cyclin E1)-CDK2 — work in concert to relieve inhibition of the dynamic transcription complex (shown in panel B) that includes RB1 and E2F. B, in G₁-phase uncommitted cells, hypo-phosphorylated RB1 binds to the E2F-transcription complex, whereas phosphorylation of RB1 by CDK2 releases RB1, thus allowing E2F-mediated S-phase genes, a requirement for DNA synthesis, to be turned on. At top, TCDD (or other planar foreign chemical) or endogenous ligand (EL) binds to AHR, which activates it to AHR*; this allows it to complex with RB1 which in turn prevents RB1 binding to E2F. AHR*-mediated up-regulation of CYP1 results in metabolic degradation of EL to the endogenous product EP. This removes EL from AHR*, inactivates AHR which releases RB1, making it then able to bind to E2F and promote G₁–>S progression. [Portions of panel A were helped by https://www.cellsignal.com/common/content/content.jsp?id=pathways-cc-g1s.]

Fig. 8

Established effects of AHR and the AHR-CYP1 axis on cell cycle functions. Arrows denote “activation or stimulation” whereas lines with a foot indicate “repression or inhibition.” A, blue circle denotes the cell cycle (G₁ –> S –> G₂ –> M –> return to the G₁ phase). The G₁/S cell cycle checkpoint controls commitment of eukaryotic cells to transition through the G₁ phase to enter into the DNA synthesis S phase. The G₂/M checkpoint precedes the cell’s entrance into mitosis, with locations indicated when cells have specific options (e.g. G₀ for the inactive, or resting, phase; versus processes such as apoptosis, differentiation, and proliferation). Two cell cycle kinase complexes — CDK4/6 (cyclin-dependent kinase 4 & 6)-CCND1 (cyclin D1), and CDK2-CCNE1 (cyclin E1) — participate as part of a dynamic transcription complex, to move the cell from G₁ to S phase (described further in panel 8B). DNA damage (upper right) activates ATM and ATR (serine-threonine kinases), and also represses MDM2 and MDM4 (MDM proto-oncogenes 2 & 4), thereby releasing their inhibition of TP53 in concert with activation of TP53 by ATM/ATR. Phosphorylation (P denotes inorganic PO₄) of TP53 by PP2A (protein phosphatase-2A), via several steps, activates PAK1–6 (p21 (RAC1; CDKN1A)-activated kinases-1 through -6), which results in repression of CDK2. Whereas CDC25A (cell division cycle-25A) activates both CDK4/6 and CDK2, CDC25A is suppressed by CHEK1/2. At the M/G₁ boundary (lower left), the CDC25B/26-CDK1 complex induces either differentiation or proliferation. Activated AHR* stimulates the complex of POU5F1 (POU class-5 homeobox-1; formerly OCT4) and SOX2 (SRY-box-2), which in turn up-regulates MID1 (midline-1), thus allowing MID1 to activate mitosis. For the sake of avoiding clutter, many additional factors participating in the cell cycle are not shown. The two cell cycle kinase complexes — CDK4/6-CCND1 (cyclin D1) and CDK2-CCNE1 (cyclin E1)-CDK2 — work in concert to relieve inhibition of the dynamic transcription complex (shown in panel B) that includes RB1 and E2F. B, in G₁-phase uncommitted cells, hypo-phosphorylated RB1 binds to the E2F-transcription complex, whereas phosphorylation of RB1 by CDK2 releases RB1, thus allowing E2F-mediated S-phase genes, a requirement for DNA synthesis, to be turned on. At top, TCDD (or other planar foreign chemical) or endogenous ligand (EL) binds to AHR, which activates it to AHR*; this allows it to complex with RB1 which in turn prevents RB1 binding to E2F. AHR*-mediated up-regulation of CYP1 results in metabolic degradation of EL to the endogenous product EP. This removes EL from AHR*, inactivates AHR which releases RB1, making it then able to bind to E2F and promote G₁–>S progression. [Portions of panel A were helped by https://www.cellsignal.com/common/content/content.jsp?id=pathways-cc-g1s.]

Fig. 9

Overall scheme postulated to operate for some, perhaps all, of the bHLH/PAS sensors. A, generalized diagram. B, specific scheme for the AHR-CYP1 axis. ELs, endogenous ligands. See text for details.

Fig. 9

Overall scheme postulated to operate for some, perhaps all, of the bHLH/PAS sensors. A, generalized diagram. B, specific scheme for the AHR-CYP1 axis. ELs, endogenous ligands. See text for details.