Regulatory mechanism of brassinosteroid-responsive gene expression by the bHLH-like transcription factor BIL1/BZR1, with non-canonical dimeric structure

Abstract

Brassinosteroids (BRs) are essential phytohormones that regulate a broad range of physiological processes. BR signaling activates BIL1/BZR1 of the plant-specific bHLH-like transcription factor family. BR-responsive gene expression is directly regulated by BIL1/BZR1 in both activation and repression. Here we describe a non-canonical dimeric structure that gives rise to a unique DNA recognition mechanism for BIL1/BZR1. This structure fine-tunes the Glu(i) residue in the direction that loosens the recognition of the C₁A₂ bases of the G-box motif (5´-CACGTG-3´) and tightens a hydrogen bonding network with the phosphate groups of DNA. Consequently, BIL1/BZR1 binds to the NN-BRRE-core motif (5´-NNCGTG-3´) and exerts selectivity for two nucleobases flanking the motif by the DNA shape readout without direct recognition of the nucleobases. Our genome-wide data analysis also shows that the tight binding of BIL1/BZR1 alone to gene promoters is required for BR-responsive transcriptional repression but not for transcriptional activation.