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WRKY protein domain
The WRKY domain is found in the WRKY transcription factor family, a class of transcription factors.〔Rushton, Torres, Parniske, Wernert, Hahlbrock, et al. (1996) Interaction of elicitor-induced DNA-binding proteins with elicitor response elements in the promoters of parsley PR1 genes. The EMBO Journal. 15(20). 5690, Eulgem, Rushton, Robatzek and Somssich (2000) The WRKY superfamily of plant transcription factors. Trends in Plant Science. 5(5). 199-206〕 The WRKY domain is found almost exclusively in plants although WRKY genes appear present in some diplomonads, social amoebae and other amoebozoa, and fungi incertae sedis. They appear absent in other non-plant species. WRKY transcription factors have been a significant area of plant research for the past 20 years.〔Schluttenhofer and Yuan (2014) Regulation of Specialized Metabolism by WRKY Transcription Factors. Plant Physiology, Bakshi and Oelmüller (2014) WRKY transcription factors: Jack of many trades in plants. Plant Signaling & Behavior. 9(1). e27700〕 The WRKY DNA-binding domain recognizes the W-box (T)TGAC(C/T) (and variants of this sequence) cis-regulatory element.
==Structure==
WRKY transcription factors contain either one or two WRKY protein domains. The WRKY protein domain is 60 to 70 amino acids long type of DNA binding domain. The domain is characterized by a highly conserved core WRKYGQK motif and a zinc finger region. The cysteine and histidine zinc finger domain occurs as a CX4-5CX22-23HXH or CX7CX23HXC type, where X can be any amino acid.〔Eulgem, Rushton, Robatzek and Somssich (2000) The WRKY superfamily of plant transcription factors. Trends in Plant Science. 5(5). 199-206〕 The zinc finger binds a Zn+2 ion, which is required for protein function.〔Yamasaki, Kigawa, Inoue, Tateno, Yamasaki, et al. (2005) Solution Structure of an Arabidopsis WRKY DNA Binding Domain. The Plant Cell. 17(3). 944-956〕 While the WRKYGQK is highly conserved in most WRKY domains, variation in the core sequence has been documented.〔Schluttenhofer and Yuan (2014) Regulation of Specialized Metabolism by WRKY Transcription Factors. Plant Physiology, Zhang and Wang (2005) The WRKY transcription factor superfamily: its origin in eukaryotes and expansion in plants. BMC Evolutionary Biology. 5(1). 1〕 A frequently occurring variant of the core sequence is WRKYGKK, which is present in most plant species.〔Eulgem, Rushton, Robatzek and Somssich (2000) The WRKY superfamily of plant transcription factors. Trends in Plant Science. 5(5). 199-206, Schluttenhofer and Yuan (2014) Regulation of Specialized Metabolism by WRKY Transcription Factors. Plant Physiology, Zhang and Wang (2005) The WRKY transcription factor superfamily: its origin in eukaryotes and expansion in plants. BMC Evolutionary Biology. 5(1). 1, Song, Wang, Nan and Wang (2014) The WRKY Transcription Factor Genes in Lotus japonicus. International Journal of Genomics. 2014(15, Xiong, Xu, Zhang, Wu, Chen, et al. (2013) Genome-wide analysis of the WRKY gene family in physic nut (Jatropha curcas L.). Gene. 524(2). 124-132〕
The structure of the WRKY protein domain was first determined in 2005 using nuclear magnetic resonance (NMR) and later by crystallography.〔Yamasaki, Kigawa, Inoue, Tateno, Yamasaki, et al. (2005) Solution Structure of an Arabidopsis WRKY DNA Binding Domain. The Plant Cell. 17(3). 944-956, Duan, Nan, Liang, Mao, Lu, et al. (2007) DNA binding mechanism revealed by high resolution crystal structure of Arabidopsis thaliana WRKY1 protein. Nucleic Acids Research. 35(4). 1145-1154〕 The WRKY protein domain is a globular shape composed of five anti-parallel β-strands. The core WRKYGQK motif is found on the second β-strand.〔Duan, Nan, Liang, Mao, Lu, et al. (2007) DNA binding mechanism revealed by high resolution crystal structure of Arabidopsis thaliana WRKY1 protein. Nucleic Acids Research. 35(4). 1145-1154〕 Eighteen amino acids are highly conserved in the WRKY protein domain, including the core motif, zinc-finger binding cysteines and histidines, and a triad forming a DWK salt bridge.〔Duan, Nan, Liang, Mao, Lu, et al. (2007) DNA binding mechanism revealed by high resolution crystal structure of Arabidopsis thaliana WRKY1 protein. Nucleic Acids Research. 35(4). 1145-1154〕 The triad consist of a conserved tryptophan (W) of the core motif, along with a aspartic acid (D) four amino acids upstream and a lysine (K) 29 amino acids downstream of it, stabilizing the entire domain.〔Duan, Nan, Liang, Mao, Lu, et al. (2007) DNA binding mechanism revealed by high resolution crystal structure of Arabidopsis thaliana WRKY1 protein. Nucleic Acids Research. 35(4). 1145-1154〕 Five amino acids on the third β-strand (PRSYY) are also well conserved in the WRKY domain.〔Duan, Nan, Liang, Mao, Lu, et al. (2007) DNA binding mechanism revealed by high resolution crystal structure of Arabidopsis thaliana WRKY1 protein. Nucleic Acids Research. 35(4). 1145-1154〕 Importantly, the WRKY genes contain a conserved intron in the WRKY domain, which occurs at the location encoding for the PR of the PRSYY amino acid sequence,〔Eulgem, Rushton, Robatzek and Somssich (2000) The WRKY superfamily of plant transcription factors. Trends in Plant Science. 5(5). 199-206〕 thus explaining the conservation of this motif.
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