Phylogenetic Analyses Of Vitis Vinifera WRKY Gene Superfamily

WRKY transcription factors are a group of inducible transcription factors which are involved in a variety of stress responses. There is a conserved WRKYGQK amino acids sequence in N-terminal of the proteins. There is a conserved WRKYGQK amino acids sequence in N-terminal of the proteins. WRKY transcription factors regulate the expression of the target genes by binding to the W-box, a cis-element with (T)(T)TGAC(C/T) sequence in the genes promoter regions. Therefore, the WRKY transcription factors are involved in various physiological and biochemical responses in the plant. More than 600 members of WRKYs were reported and most of them were found in model plants such as arabidopsis and rice. Using the methods of bioinformatics, the study want to get complete WRKY super family in Vitis vinifera by analyzing its genome. The article analyzes the evolution of WRKY super family in Vitis vinifera, which could provide some useful information for its following function research. The results of this study are as follows:1. 56 VvWRKY genes are predicted by adopting two search methods in NCBI database, predicting ORF using the tool ORF finder, checking up by the tools Pfam and CDD, and locating in Vitis vinifera genome by MapView. Based on the location, WRKYs are named of the Vitis vinifera as VvWRKY1-VvWRKY56(except VvWRKY1 and VvWRKY2), complete VvWRKYs are obtained relatively.2. The phylgenetic trees are constructed by ClustalX(1.83) and further by MEGA4(Bata) using WRKY conserved domains and WRKY genes respectively. The two phylogenetic trees are clusterd in a similar manner, which shows WRKY conserved domains represent the evolution of WRKY genes to some extent and also shows WRKY conserved domain is the important functional and evolutional unit of WRKY transcription factors. The classification system is based on both of the features of zinc fingers and phylogenetic tree of WRKY conserved domains. The VvWRKY gene family can be classified as three groups and five subgroups(subgroupâ… a andâ… b in groupâ… , groupâ…¡, subgroupâ…¢a,â…¢b,â…¢c in groupâ…¢).3. The paper further analyzed WRKY conserved domain in the groups and subgroups. The structure mode of amino acid are obtained. Two kinds of variation are found which are WRKYGKK and WREYGOK in core sequences WRKYGQK. The structure mode of zinc finger has four kind which are C-X4-C-X22-HXH, C-X4-C-X23-HXH, C-X5-C-X23-HXH and C-X7-C-X23-HTC. 4. During prediction of the WRKY conserved domains by CDD, we found some other zinc finger out of the conserved domain. According to the alignment by ClustalX (1.83), they are completely different from the zinc finger in the WRKY conserved domain. They belong to WRKY-GCM super family and all in subgroupâ…¢b. The existence of this kind of zinc finger may enhance the effect of WRKY protein in the plant defense.5. By searching in the UniGene database of NCBI with the number of locus, expression profile of WRKY genes are gained. Some genes could find the expression but some couldn't. VvWRKY genes may express in many organs such as bud, cell culture, flower, fruit, inflorescence, leaf, pedicel, root and stem. Different genes express in different organs, so do expression level.