Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10-12, 08028 Barcelona, Spain; Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Baldiri Reixac 10-12, 08028 Barcelona, Spain.
Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, the Netherlands.
Cell. 2014 Jan 30;156(3):577-89. doi: 10.1016/j.cell.2013.12.027.
Auxin regulates numerous plant developmental processes by controlling gene expression via a family of functionally distinct DNA-binding auxin response factors (ARFs), yet the mechanistic basis for generating specificity in auxin response is unknown. Here, we address this question by solving high-resolution crystal structures of the pivotal Arabidopsis developmental regulator ARF5/MONOPTEROS (MP), its divergent paralog ARF1, and a complex of ARF1 and a generic auxin response DNA element (AuxRE). We show that ARF DNA-binding domains also homodimerize to generate cooperative DNA binding, which is critical for in vivo ARF5/MP function. Strikingly, DNA-contacting residues are conserved between ARFs, and we discover that monomers have the same intrinsic specificity. ARF1 and ARF5 homodimers, however, differ in spacing tolerated between binding sites. Our data identify the DNA-binding domain as an ARF dimerization domain, suggest that ARF dimers bind complex sites as molecular calipers with ARF-specific spacing preference, and provide an atomic-scale mechanistic model for specificity in auxin response.
生长素通过一系列功能不同的 DNA 结合生长素响应因子 (ARF) 来控制基因表达，从而调节众多植物发育过程，但生长素响应特异性产生的机制尚不清楚。在这里，我们通过解析关键的拟南芥发育调节剂 ARF5/ MONOPTEROS (MP)、其分歧的同源物 ARF1 以及 ARF1 和通用生长素响应 DNA 元件 (AuxRE) 的复合物的高分辨率晶体结构来解决这个问题。我们表明，ARF 的 DNA 结合结构域也可以形成同源二聚体以产生协同的 DNA 结合，这对于体内 ARF5/MP 功能至关重要。引人注目的是，DNA 结合残基在 ARFs 之间是保守的，我们发现单体具有相同的固有特异性。然而，ARF1 和 ARF5 同源二聚体在结合位点之间允许的间隔存在差异。我们的数据将 DNA 结合结构域鉴定为 ARF 二聚化结构域，表明 ARF 二聚体作为分子卡尺结合复杂位点，具有 ARF 特异性的间隔偏好，并提供了生长素响应特异性的原子尺度机械模型。
