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TOBFAC: The database of tobacco transcription factors

Family: WRKY

Minimum number of tobacco WRKY genes: 93

Count of tobacco WRKY sequences: 110

Pfam accession: WRKY

SHOULD possess WRKY domain and COULD   possess zf-BED domain

WRKY transcription factors are one of the largest multigene families of transcriptional regulators in plants but are absent from prokaryotes, animals and fungi . Each WRKY protein has at least one WRKY domain of approximately 60 amino acids containing the conserved amino acid sequence WRKYGQK at its N-terminus (from which the factors take their name) and a novel zinc finger motif at its C-terminus . The WRKYGQK amino acid sequence forms a β-strand that directly contacts the binding site on the promoters of target genes . Usually, this binding site is the W box (C/T)TGAC(T/C), an element found in the promoters of many stress-related plant genes . The ancestral-type WRKY transcription factor (group I) contains two WRKY domains (N-terminal and C-terminal). All other genes contain one WRKY domain and are classified into groups IIa, IIb, IIc, IId, IIe and III based on their primary amino acid sequence and structure of their zinc finger motifs . Rushton et al. (1996) presented the first evidence that WRKY transcription factors play roles in plant defence. There is now considerable evidence that they play roles in responses not only to biotic stresses but also abiotic stresses such as wounding, drought and cold adaptation and in Arabidopsis, most of the 74 WRKY genes are transcriptionally upregulated by defence-related stimuli. This suggests that a major role of WRKY genes in flowering plants is to mediate defence responses . It has recently been suggested that WRKY DNA-binding domains are related to the widespread GCM1 superfamily as both contain a four-stranded fold . However, any relatedness is distant as the primary amino acid sequences show very little similarity.

Papers

Eulgem, T; Rushton, PJ; Robatzek, S; Somssich, IE. The WRKY superfamily of plant transcription factors. Trends Plant Sci. 2000. 5(5):199-206 PMID: 10785665

Rushton PJ, Torres JT, Parniske M, Wernert P, Hahlbrock K, Somssich IE. Interaction of elicitor-induced DNA-binding proteins with elicitor response elements in the promoters of parsley PR1 genes. EMBO J. 1996 Oct 15;15(20):5690-700. PMID: 8896462

Rushton PJ, Macdonald H, Huttly AK, Lazarus CM, Hooley R. Members of a new family of DNA-binding proteins bind to a conserved cis-element in the promoters of alpha-Amy2 genes. Plant Mol Biol. 1995 Nov;29(4):691-702. PMID: 8541496

This gene family is complicated by:

1. Some genes (Group I) having two domains whilst the other have one.

2. An intron that divides most domains into two, resulting in many incomplete domain sequences.

3. A very muddled set of published genes (duplicate genes with multiple accessions and duplicate names for different genes).

The Gene Space sequences.

Contigs: 93

Singletons: 20

Total domains: 113

Examination of these enabled three to be joined to other sequences. This resulted in 52, 61 and 64 being lost.

Final GSS domain total = 110 (These are the sequences currently on TOBFAC).

Published Sequences

The following published tobacco WRKY genes did not appear to be present in the GSSs.

They represent an extra 27 WRKY domains

And 18 WRKY genes

WRKY12, WRKY11, WRKY10, NtWRKY9NT, NtWRKY9CT, NtWRKY8NT, NtWRKY8CT, NtWRKY7NT, NtWRKY7CT, NtWRKY6NT, NtWRKY6CT, NtWRKY4NT, NtWRKY4CT, NtWRKY1NT, NtWRKY1CT, NtWRKY2NT, NtWRKY2CT, ACRE126, NtEIG-D48, g17-2-13, WIZZ, WRKY4, WRKY3, TMVRRG, NtWRKY3, WRKY2NT, WRKY2CT, WRKY1NT, WRKY1CT

Examination of the published and GSS sequences led to a reduction in domain number by 6 (as a result of joining some Group I genes etc.

Final number of domains – 131

Analysis of the Groups of the WRKY domains led to a final minimum number of 93 genes.

More than any other transcription family group, the WRKY family results are rather confused. Additional searches and comparisons to EST sequences should resolve many of these discrepancies.

Some genes that are not present in the GSSs may have come from different tobacco cultivars or BY-2 cells and a cleaner GSS and EST based dataset will probably be much more accurate.

Search sequences and info

Transcription factor sequences

Tobacco published genes related to transcription factor family WRKY

Authors of this site:

Paul J Rushton
Marta T. Bokowiec
Xianfeng (Jeff) Chen
Thomas (Tom) W Laudeman
Jennifer F. Brannock
Michael P. Timko

Contact:

pr8y@virginia.edu