Plant Transcription factor database - Universität Potsdam
version: 3.0

Selaginella moellendorffii WRKY Family

Description

Wu et al. 2005: WRKY transcription factors, originally isolated from plants contain one or two conserved WRKY domains, about 60 amino acid residues with the WRKYGQK sequence followed by a C2H2 or C2HC zinc finger motif. Evidence is accumulating to suggest that the WRKY proteins play significant roles in responses to biotic and abiotic stresses, and in development. In this research, we identified 102 putative WRKY genes from the rice genome and compared them with those from Arabidopsis. The WRKY genes from rice and Arabidopsis were divided into three groups with several subgroups on the basis of phylogenies and the basic structure of the WRKY domains (WDs). The phylogenetic trees generated from the WDs and the genes indicate that the WRKY gene family arose during evolution through duplication and that the dramatic amplification of rice WRKY genes in group III is due to tandem and segmental gene duplication compared with those of Arabidopsis. The result suggests that some of the rice WRKY genes in group III are evolutionarily more active than those in Arabidopsis, and may have specific roles in monocotyledonous plants. Further, it was possible to identify the presence of WRKY-like genes in protists (Giardia lamblia and Dictyostelium discoideum) and green algae Chlamydomonas reinhardtii through database research, demonstrating the ancient origin of the gene family. The results obtained by alignments of the WDs from different species and other analysis imply that domain gain and loss is a divergent force for expansion of the WRKY gene family, and that a rapid amplification of the WRKY genes predate the divergence of monocots and dicots. On the basis of these results, we believe that genes encoding a single WD may have been derived from the C-terminal WD of the genes harboring two WDs. The conserved intron splicing positions in the WDs of higher plants offer clues about WRKY gene evolution, annotation, and classification.

Members of this family
  SHOULD possess WRKY domain

Domain alignments

Benchmark against A. thaliana

The Sensitivity and Positive Predictive Value (PPV) were assessed for this family. The data reported by Ulker & Somssich 2004 for A. thaliana were taken as gold standard.

The gold standard reported 71 members for this family, 71 of which are present in ArabTFDB, giving a PPV of 0.99. One additional member not present in ArabTFDB might be false negative, giving a Sensitivity of 0.99.

This family is also present in:

References

There are 19 gene models in this family



Gene modelDescriptionDomains
108669 e_gw1.37.246.1 WRKY
125080 e_gw1.77.283.1 WRKY
147026 estExt_Genewise1.C_140317 Plant_zn_clust WRKY
24407 gw1.4.346.1 WRKY
29146 gw1.1.691.1 WRKY
29247 gw1.19.327.1 WRKY
29692 gw1.1.715.1 WRKY
29703 gw1.5.537.1 WRKY
56793 gw1.39.447.1 WRKY
66769 gw1.11.1052.1 WRKY
69405 gw1.4.1622.1 WRKY
69423 gw1.8.1554.1 WRKY
69431 gw1.0.1823.1 WRKY
73220 gw1.4.1722.1 WRKY
73221 gw1.14.1023.1 WRKY
73225 gw1.14.1024.1 WRKY
77979 e_gw1.2.656.1 WRKY
81371 e_gw1.4.1665.1 WRKY
92733 e_gw1.13.308.1 WRKY

General references

Eulgem, T; Rushton, PJ; Robatzek, S; Somssich, IE. 2000. The WRKY superfamily of plant transcription factors. Trends Plant Sci. 5(5):199-206 PUBMEDID:10785665
Ulker, B; Somssich, IE. 2004. WRKY transcription factors: from DNA binding towards biological function. Curr. Opin. Plant Biol. 7(5):491-8 PUBMEDID:15337090
Zhang, Y; Wang, L. 2005. The WRKY transcription factor superfamily: its origin in eukaryotes and expansion in plants. BMC Evol. Biol. 5(1):1 PUBMEDID:15629062