Chen Wan, Yan Wei, Jiang Kai, Huang Hongda
Institute for Biological Electron Microscopy, Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China.
New Cornerstone Science Laboratory, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.
Plant Physiol. 2025 Jul 3;198(3). doi: 10.1093/plphys/kiaf292.
Homeodomain-leucine zipper (HD-Zip) genes encode a large family of plant-specific transcription factors (TFs) that are integral to plant development, growth, regulation, and responses to environmental and hormonal signals. While the roles and mechanisms of HD-Zip TFs have been extensively studied, the structural basis for their DNA recognition remains unclear. In this study, we analyzed DAP-seq data and identified consensus DNA motifs, 5'-AAT[W]AT-3' and 5'-[N]AAA[N][N]-3', preferentially bound by HD-Zip TFs. Both motifs feature a 5'-AA(T/A)-3' core, which is shared across previously identified HD-Zip target sequences, suggesting a common recognition feature within the HD-Zip family. Focusing on the well-characterized HD-Zip IV TF PROTEIN PRODUCTION FACTOR 2 (PDF2) from Arabidopsis (Arabidopsis thaliana) and its interaction with the L1 box DNA sequence, our structural and biochemical analyses revealed that the PDF2 HD-ZA module forms a dimer to specifically recognize the 5'-AATG-3' core through an asymmetric binding mode. In this mode, only the primary recognition helix of 1 protomer and the N-arm of the other protomer in the PDF2 HD-ZA dimer are involved in specific DNA interactions. Our study offers insights into the molecular mechanisms of HD-Zip TFs and provides a structural template for engineering applications in agricultural research.
同源异型域-亮氨酸拉链（HD-Zip）基因编码一大类植物特有的转录因子（TFs），这些转录因子对于植物的发育、生长、调控以及对环境和激素信号的响应至关重要。虽然HD-Zip转录因子的作用和机制已得到广泛研究，但其DNA识别的结构基础仍不清楚。在本研究中，我们分析了DAP-seq数据并鉴定出共有DNA基序，即5'-AAT[W]AT-3'和5'-[N]AAA[N][N]-3'，它们优先被HD-Zip转录因子结合。这两个基序都具有一个5'-AA(T/A)-3'核心，该核心在先前鉴定的HD-Zip靶序列中是共有的，这表明HD-Zip家族内存在共同的识别特征。以拟南芥中特征明确的HD-Zip IV转录因子蛋白质生产因子2（PDF2）及其与L1盒DNA序列的相互作用为重点，我们的结构和生化分析表明，PDF2 HD-ZA模块形成二聚体，通过不对称结合模式特异性识别5'-AATG-3'核心。在这种模式下，PDF2 HD-ZA二聚体中只有一个亚基的主要识别螺旋和另一个亚基的N臂参与特异性DNA相互作用。我们的研究为HD-Zip转录因子的分子机制提供了见解，并为农业研究中的工程应用提供了结构模板。
