Plant Transcription factor database - Universität Potsdam
version: 3.0

Physcomitrella patens 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 37 gene models in this family



Gene modelDescriptionDomains
104466 estExt_fgenesh1_pm.C_70002 WRKY
114886 e_gw1.11.168.1 WRKY
118564 e_gw1.25.129.1 WRKY
121365 e_gw1.35.333.1 WRKY
122251 e_gw1.39.143.1 WRKY
122959 e_gw1.42.180.1 WRKY
124219 e_gw1.48.6.1 WRKY
129018 e_gw1.73.71.1 WRKY
137776 e_gw1.140.97.1 WRKY
139623 e_gw1.158.71.1 WRKY
139677 e_gw1.159.68.1 WRKY
140129 e_gw1.163.7.1 WRKY
145911 e_gw1.235.59.1 WRKY
154002 e_gw1.407.30.1 WRKY
15794 gw1.135.38.1 WRKY
165218 estExt_fgenesh1_pg.C_840061 WRKY
18161 gw1.157.36.1 WRKY
19197 gw1.115.63.1 WRKY
19202 gw1.166.27.1 WRKY
19217 gw1.137.58.1 WRKY
19842 gw1.109.45.1 WRKY
210806 estExt_Genewise1.C_650158 WRKY
26902 gw1.35.201.1 WRKY
29585 gw1.39.164.1 WRKY
29606 gw1.13.215.1 WRKY
29874 gw1.47.186.1 WRKY
38878 gw1.426.49.1 WRKY
49643 gw1.198.128.1 WRKY
54343 gw1.5.658.1 WRKY
64403 fgenesh1_pg.scaffold_2000280 WRKY
72378 fgenesh1_pg.scaffold_36000177 WRKY
8693 gw1.426.27.1 WRKY
90300 fgenesh1_pg.scaffold_195000041 WRKY
93078 fgenesh1_pg.scaffold_236000008 WRKY
95428 fgenesh1_pg.scaffold_280000027 WRKY
9551 gw1.244.25.1 WRKY
9656 gw1.246.77.1 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