Crystal Structure of E47−NeuroD1/Beta2 bHLH Domain−DNA Complex:  Heterodimer Selectivity and DNA Recognition^,

Abstract

The ubiquitous class I basic helix-loop-helix (bHLH) factor E47 forms heterodimers with multiple tissue specific class II bHLH proteins to regulate distinct differentiation pathways. In order to define how class I- class II heterodimer partners are selected, we determined the crystal structure of the E47-NeuroD1-bHLH dimer in complex with the insulin promoter E-box sequence. Purification of the bHLH domain of E47-NeuroD1 indicates that E47 heterodimers are stable in solution. The interactions between E47 and NeuroD1 in the heterodimer are comparable to the interactions between E47 monomers in the homodimer, including hydrogen bonding, buried hydrophobic surface, and packing interactions. This is consistent with a model in which E47-NeuroD1 heterodimers are favored due to the instability of NeuroD1 homodimers. Although E47-NeuroD1 is oriented uniquely on the E-box sequence (CATCTG) within the promoter of the insulin gene, no direct contacts are observed with the central base pairs within this E-box sequence. We propose that concerted domain motions allow E47 to form specific base contacts in solution. NeuroD1 is restrained from adopting the same base contacts by an additional phosphate backbone interaction by the neurogenic-specific residue His115. Orienting E47-NeuroD1 on promoters may foster protein-protein contacts essential to initiate transcription.

Zinc ions upregulate the hormone gastrin via an E-box motif in the proximal gastrin promoter

“…Our result that Zn 2C ions induce gastrin expression through the activation of an E-box binding transcription factor via the phosphorylation of AKT raises the possibility that Zn 2C may induce the EMT through direct activation of E-boxbinding transcription factors. Although further studies of the transcription factors involved are warranted, in the light of evidence that many known (Longo et al 2008, Terragni et al 2011 and as yet uncharacterized transcription factors (Biggs et al 2007) can bind E-boxes it is beyond the scope of the current study to identify one single transcription factor which activates gastrin expression in response to Zn 2C . What does our finding that gastrin is induced by Zn 2C ions imply about normal gastric physiology?…”

Retinoic acid signaling and neuronal differentiation

“…Id proteins are intrinsically linked to the cell cycle in neurogenesis. Id2 inhibits bHLH factor E47 [156], which prevents heterodimerization of E47 with NeuroD1 [157]. An important downstream target of E47 is the CIK p57 Kip2 ; hence, Id2 effectively down-regulates p57 Kip2 via E47 inhibition, thus promoting proliferation in neuroblastoma cells [156].…”

A direct fate exclusion mechanism by Sonic hedgehog-regulated transcriptional repressors

“…RNA samples were collected up to 24 h post-Dox induction and subjected to RNA-seq or BioMark (Fluidigm) RT-qPCR assay. RNAseq was performed at 12 h post-induction in biological duplicates, and analyzed with STAR aligner and DEseq2 (GEO accession number: GSE65462 Longo et al (2008)]. See supplementary material Table S3 for RT-qPCR primer sequences.…”