Assembly and function of bHLH–PAS complexes

Abstract

The basic helix-loop-helix-PER-ARNT-SIM (bHLH-PAS) family of transcription factors coordinates the expression of distinct transcriptional programs to control processes from development to the hypoxia response and beyond. 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 bHLH-PAS family is defined by formation of heterodimers comprising class I and class II subunits. Class I proteins are typically regulated by tissue or environmental-specific factors, whereas class II proteins are expressed ubiquitously. Examples of class I proteins include AHR (regulated by xenobiotics), hypoxiainducible factor-α (HIF-α, regulated by hypoxia), neuronal PAS domain proteins (NPAS, developmentally regulated), and circadian locomotor output cycles protein kaput (CLOCK, circadian rhythms). ARNT is the predominant class II subunit found in bHLH-PAS complexes, whereas the related protein brain and muscle ARNTlike 1 (BMAL1) appears to be primarily dedicated to CLOCK to regulate circadian rhythms. Although cellular studies have largely outlined the different regulatory mechanisms that control heterodimerization, subcellular localization, and activity of these complexes, the structural basis for their assembly and diverse functions has been unclear.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. 1). Notably, the PAS-A domains of AHR, NPAS3, and HIF1-α all make direct contacts with their own bHLH domains that tether the N-terminal PAS domain in close proximity to DNA. It appears that ARNT and BMAL1 confer distinct differences in the global architecture of the bHLH-PAS heterodimers via the spatial arrangement of their PAS domains (Fig. 1). Specifically, the PAS-A and PAS-B domains of ARNT are completely separated in space from one other, whereas the PAS domains of BMAL1 make numerous interdomain contacts that orient the CLOCK-BMAL1 heterodimer more linearly away from DNA (2, 5). Although the structure of AHR-ARNT by Seok et al. (1) lacks the PAS-B domains, its similarity in packing of the AHR and ARNT PAS-A domains suggests that the ove...

Structural insights and characterization of human Npas4 protein

“…This can further be implicated to enhance conformational plasticity of Npas4 which may help in behaving differently to various transcription factors and enhancing its functional repertoire. The presence of IDRs C-terminal regulatory domain have also been reported in other Bhlh proteins ( Fribourgh & Partch, 2017 ).…”

Peer Review #1 of "Structural insights and characterization of human Npas4 protein (v0.1)"

“…This can further be implicated to enhance conformational plasticity of Npas4 which may help in behaving differently to various transcription factors and enhancing its functional repertoire. The presence of IDRs C-terminal regulatory domain have also been reported in other Bhlh proteins (Fribourgh & Partch 2017) Moreover, previous reported behavior of IDRs suggest that the presence of more charged residues enhances electrostatic interactions which augments the propensity of post translational modifications (Hofmann et al 2012;Mao et al 2010). This subsequently resulted in altered binding affinities and increased range of structural heterogeneity derived from disorder to order transitions altering protein compactness.…”

Genome-wide analyses of the bHLH superfamily in crustaceans: reappraisal of higher-order groupings and evidence for lineage-specific duplications

“…Many well-known PAS proteins have been shown to also possess a bHLH domain where they are collectively termed as bHLH-PAS [ 11 , 28 ]. The bHLH-PAS family is further classified into two subgroups: α-class and β-class [ 11 , 51 ]. The α-class proteins act as archetypal sensors of tissue-specific or environmental signals, e.g.…”

“…single-minded (SIM-development), HIF (oxygen sensing), neuronal PAS domain proteins (NPAS-development) and circadian locomotor output cycles protein kaput (CLOCK-circadian timekeeping) and MET (juvenile hormone signalling) [ 11 , 51 – 53 ]. Unable to dimerise among themselves, α-class members require β-class proteins, aryl hydrocarbon receptor nuclear translocators (ARNT), as their broad-spectrum binding partners [ 11 , 51 ]. We perform phylogenetic analysis on bHLH-PAS members identified from decapods and basal crustaceans (branchiopods and copepods; figure 3 ; electronic supplementary material, figures S4 and S5).…”