Department of Plant Physiology, Center for Plant Molecular Biology, University of Tübingen, 72076 Tübingen, Germany and Department of Computer Science, Applied Bioinformatics, Center for Bioinformatics, Quantitative Biology Center, University of Tübingen, 72076 Tübingen, Germany.
Nucleic Acids Res. 2013 Nov;41(21):9764-78. doi: 10.1093/nar/gkt732. Epub 2013 Aug 23.
WRKY transcription factors constitute a large protein family in plants that is involved in the regulation of developmental processes and responses to biotic or abiotic stimuli. The question arises how stimulus-specific responses are mediated given that the highly conserved WRKY DNA-binding domain (DBD) exclusively recognizes the 'TTGACY' W-box consensus. We speculated that the W-box consensus might be more degenerate and yet undetected differences in the W-box consensus of WRKYs of different evolutionary descent exist. The phylogenetic analysis of WRKY DBDs suggests that they evolved from an ancestral group IIc-like WRKY early in the eukaryote lineage. A direct descent of group IIc WRKYs supports a monophyletic origin of all other group II and III WRKYs from group I by loss of an N-terminal DBD. Group I WRKYs are of paraphyletic descent and evolved multiple times independently. By homology modeling, molecular dynamics simulations and in vitro DNA-protein interaction-enzyme-linked immunosorbent assay with AtWRKY50 (IIc), AtWRKY33 (I) and AtWRKY11 (IId) DBDs, we revealed differences in DNA-binding specificities. Our data imply that other components are essentially required besides the W-box-specific binding to DNA to facilitate a stimulus-specific WRKY function.
WRKY 转录因子是植物中一个庞大的蛋白质家族，参与调控发育过程以及对生物或非生物刺激的响应。问题是，鉴于高度保守的 WRKY DNA 结合域 (DBD) 仅特异性识别“TTGACY”W 框共识序列，那么如何介导刺激特异性响应。我们推测 W 框共识序列可能更加退化，而且不同进化起源的 WRKY 的 W 框共识序列存在尚未检测到的差异。WRKY DBD 的系统发育分析表明，它们起源于真核生物谱系早期的一个祖先 IIc 样 WRKY。IIc WRKY 的直系同源支持所有其他 II 和 III WRKY 都由 I 组通过缺失 N 端 DBD 而从 I 组单一起源而来。I 组 WRKY 是并系发生的，并且独立多次进化而来。通过同源建模、分子动力学模拟以及体外 DNA-蛋白质相互作用-酶联免疫吸附试验，我们揭示了 AtWRKY50（IIc）、AtWRKY33（I）和 AtWRKY11（IId）DBD 之间的 DNA 结合特异性差异。我们的数据表明，除了特异性结合 DNA 的 W 框之外，还需要其他基本成分来促进刺激特异性 WRKY 功能。
