6YCQ

Crystal structure of the DNA binding domain of Arabidopsis thaliana Auxin Response Factor 1 (AtARF1) in complex with High Affinity DNA

6YCQ の概要

• エントリーDOI: 10.2210/pdb6ycq/pdb
• 分子名称: Auxin response factor 1, 21-7A, 21-7B, ... (8 entities in total)
• 機能のキーワード: transcription factor, dna binding, nucleus, hormone response, transcription
• 由来する生物種: Arabidopsis thaliana (thale cress); 詳細
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 96091.04

構造登録者

Crespo, I.,Weijers, D.,Boer, D.R. (登録日: 2020-03-18, 公開日: 2020-09-09, 最終更新日: 2024-01-24)

主引用文献

Freire-Rios, A.,Tanaka, K.,Crespo, I.,van der Wijk, E.,Sizentsova, Y.,Levitsky, V.,Lindhoud, S.,Fontana, M.,Hohlbein, J.,Boer, D.R.,Mironova, V.,Weijers, D.
Architecture of DNA elements mediating ARF transcription factor binding and auxin-responsive gene expression in Arabidopsis .
Proc.Natl.Acad.Sci.USA, 117:24557-24566, 2020

PubMed Abstract: The hormone auxin controls many aspects of the plant life cycle by regulating the expression of thousands of genes. The transcriptional output of the nuclear auxin signaling pathway is determined by the activity of AUXIN RESPONSE transcription FACTORs (ARFs), through their binding to -regulatory elements in auxin-responsive genes. Crystal structures, in vitro, and heterologous studies have fueled a model in which ARF dimers bind with high affinity to distinctly spaced repeats of canonical AuxRE motifs. However, the relevance of this "caliper" model, and the mechanisms underlying the binding affinities in vivo, have remained elusive. Here we biochemically and functionally interrogate modes of ARF-DNA interaction. We show that a single additional hydrogen bond in ARF1 confers high-affinity binding to individual DNA sites. We demonstrate the importance of AuxRE cooperativity within repeats in the and promoters in vivo. Meta-analysis of transcriptomes further reveals strong genome-wide association of auxin response with both inverted (IR) and direct (DR) AuxRE repeats, which we experimentally validated. The association of these elements with auxin-induced up-regulation (DR and IR) or down-regulation (IR) was correlated with differential binding affinities of A-class and B-class ARFs, respectively, suggesting a mechanistic basis for the distinct activity of these repeats. Our results support the relevance of high-affinity binding of ARF transcription factors to uniquely spaced DNA elements in vivo, and suggest that differential binding affinities of ARF subfamilies underlie diversity in element function.

PubMed: 32929017
DOI: 10.1073/pnas.2009554117

実験手法

X-RAY DIFFRACTION (1.65 Å)