WRKY Genomic sequences WRKY Phylogeny file WRKY Phylogeny file with bootstrap WRKY Phylogeny JPEG WRKY Phylogeny PDF

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
Locus
Description
NCBI
WRKY_1 [alias=NtWRKY1] ET049607
WRKY_2 [alias=NtWRKY2] ET051394
WRKY_3 [alias=NtWRKY3] ET048692
WRKY_4 [alias=NtWRKY4] ET047861
WRKY_5 [alias=NtWRKY5] ET042430
ET042218
WRKY_6 [alias=NtWRKY6] ET051055
ET051054
WRKY_7 [alias=NtWRKY7] ET051866
ET047162
WRKY_8 [alias=NtWRKY8] ET046378
ET044059
WRKY_9 [alias=NtWRKY9] ET050731
ET050696
WRKY_10 [alias=NtWRKY10] ET050209
ET042372
WRKY_11 [alias=NtWRKY11] ET047400
ET044252
WRKY_12 [alias=NtWRKY12] ET043684
ET043683
WRKY_13 [alias=NtWRKY13] ET046679
ET046678
WRKY_14 [alias=NtWRKY14] ET049395
ET048958
WRKY_15 [alias=NtWRKY15] ET043044
ET046178
WRKY_16 [alias=NtWRKY16] ET051755
ET047124
WRKY_17 [alias=NtWRKY17] ET049579
ET044434
WRKY_18 [alias=NtWRKY18] ET048819
ET048008
WRKY_19 [alias=NtWRKY19] ET047197
ET050091
WRKY_20 [alias=NtWRKY20] ET042030
ET050363
WRKY_21 [alias=NtWRKY21] ET047011
ET042464
WRKY_22 [alias=NtWRKY22] ET045579
ET047435
WRKY_23 [alias=NtWRKY23] ET051817
ET051893
WRKY_24 [alias=NtWRKY24] ET049290
ET050670
WRKY_25 [alias=NtWRKY25] ET048983
ET048982
WRKY_26 [alias=NtWRKY26] ET051809
ET045674
WRKY_27 [alias=NtWRKY27] ET050573
ET051445
ET048109
WRKY_28 [alias=NtWRKY28] ET046329
ET043311
ET051216
WRKY_29 [alias=NtWRKY29] ET050310
ET046815
ET048602
WRKY_30 [alias=NtWRKY30] ET049906
ET048239
ET051336
WRKY_31 [alias=NtWRKY31] ET049367
ET048909
ET048908
WRKY_32 [alias=NtWRKY32] ET051449
ET050317
ET043961
WRKY_33 [alias=NtWRKY33] ET050770
ET044574
ET044978
WRKY_34 [alias=NtWRKY34] ET048072
ET051682
ET047264
WRKY_35 [alias=NtWRKY35] ET049244
ET048736
ET050063
WRKY_36 [alias=NtWRKY36] ET049847
ET044484
ET048818
WRKY_37 [alias=NtWRKY37] ET043900
ET043899
ET047922
WRKY_38 [alias=NtWRKY38] ET044841
ET048735
ET048817
WRKY_39 [alias=NtWRKY39] ET049275
ET047949
ET049784
WRKY_40 [alias=NtWRKY40] ET046949
ET046950
ET044798
WRKY_41 [alias=NtWRKY41] ET048570
ET047950
ET048569
WRKY_42 [alias=NtWRKY42] ET044010
ET051708
ET051706
WRKY_43 [alias=NtWRKY43] ET046480
ET042099
ET044974
WRKY_44 [alias=NtWRKY44] ET045591
ET050234
ET043150
WRKY_45 [alias=NtWRKY45] ET048057
ET043669
ET044281
WRKY_46 [alias=NtWRKY46] ET050214
ET045603
ET048185
WRKY_47 [alias=NtWRKY47] ET047653
ET050082
ET048001
WRKY_48 [alias=NtWRKY48] ET045303
ET049696
ET048240
WRKY_49 [alias=NtWRKY49] ET046311
ET047920
ET047654
WRKY_50 [alias=NtWRKY50] ET050370
ET048297
ET050465
WRKY_51 [alias=NtWRKY51] ET050690
ET043803
ET047845
WRKY_53 [alias=NtWRKY53] ET047196
ET046986
ET044909
WRKY_54 [alias=NtWRKY54] ET047225
ET047226
ET047796
ET047797
WRKY_55 [alias=NtWRKY55] ET044979
ET051605
ET050534
ET047518
WRKY_56 [alias=NtWRKY56] ET050233
ET049677
ET048414
ET047851
WRKY_57 [alias=NtWRKY57] ET046739
ET046740
ET046738
ET043251
WRKY_58 [alias=NtWRKY58] ET047027
ET048052
ET049794
ET043581
WRKY_59 [alias=NtWRKY59] ET049394
ET042715
ET051503
ET044269
WRKY_60 [alias=NtWRKY60] ET047865
ET047866
ET042487
ET050417
WRKY_62 [alias=NtWRKY62] ET048535
ET046431
ET044728
ET044363
ET046306
WRKY_63 [alias=NtWRKY63] ET042845
ET051684
ET042956
ET044758
ET050741
WRKY_65 [alias=NtWRKY65] ET050103
ET043066
ET048252
ET051210
ET047020
WRKY_66 [alias=NtWRKY66] ET049922
ET049923
ET048436
ET050204
ET048850
WRKY_67 [alias=NtWRKY67] ET044977
ET051312
ET044511
ET048674
ET050027
WRKY_68 [alias=NtWRKY68] ET047764
ET051632
ET042291
ET047765
ET044491
WRKY_69 [alias=NtWRKY69] ET042376
ET047068
ET046159
ET051329
ET050467
WRKY_70 [alias=NtWRKY70] ET048371
ET043797
ET043376
ET045913
ET048370
WRKY_71 [alias=NtWRKY71] ET041834
ET051875
ET048161
ET050275
ET042140
WRKY_72 [alias=NtWRKY72] ET044257
ET045597
ET048825
ET049205
ET048866
WRKY_73 [alias=NtWRKY73] ET045252
ET049362
ET050278
ET046266
ET051651
ET048274
WRKY_74 [alias=NtWRKY74] ET045705
ET048303
ET045741
ET041986
ET043731
ET041985
WRKY_75 [alias=NtWRKY75] ET047325
ET045921
ET044042
ET045848
ET047161
ET045922
WRKY_76 [alias=NtWRKY76] ET051466
ET047049
ET048541
ET050007
ET047468
ET044521
WRKY_77 [alias=NtWRKY77] ET045118
ET043850
ET047869
ET051311
ET051529
ET048204
WRKY_78 [alias=NtWRKY78] ET046426
ET049528
ET051852
ET043166
ET043297
ET042892
WRKY_79 [alias=NtWRKY79] ET047018
ET047019
ET047803
ET050468
ET047802
ET044807
WRKY_80 [alias=NtWRKY80] ET049517
ET047281
ET043089
ET043088
ET045940
ET044738
ET044739
WRKY_81 [alias=NtWRKY81] ET044813
ET045339
ET051828
ET044814
ET047685
ET043230
ET047686
WRKY_82 [alias=NtWRKY82] ET041868
ET051885
ET044902
ET048428
ET046642
ET047366
ET051644
WRKY_83 [alias=NtWRKY83] ET042824
ET051381
ET051541
ET049567
ET051380
ET042823
ET049229
ET046377
WRKY_84 [alias=NtWRKY84] ET050643
ET043207
ET043424
ET048336
ET043128
ET043127
ET048393
ET043425
ET043126
WRKY_85 [alias=NtWRKY85] ET050719
ET044877
ET049768
ET042971
ET048991
ET048992
ET049767
ET044166
ET048741
WRKY_86 [alias=NtWRKY86] ET044747
ET047329
ET048164
ET049188
ET047330
ET048224
ET050036
ET048673
ET043667
WRKY_87 [alias=NtWRKY87] ET050167
ET049251
ET045389
ET042698
ET051348
ET045660
ET048358
ET049250
ET045388
WRKY_88 [alias=NtWRKY88] ET045275
ET042573
ET048438
ET049844
ET041895
ET047365
ET043564
ET045274
ET050782
WRKY_89 [alias=NtWRKY89] ET042547
ET044608
ET043561
ET048150
ET042546
ET041873
ET044655
ET048489
ET044607
ET045791
ET047246
WRKY_90 [alias=NtWRKY90] ET047062
ET043460
ET050724
ET051264
ET050989
ET051214
ET045828
ET047472
ET051094
ET051265
ET041854
WRKY_91 [alias=NtWRKY91] ET046437
ET046997
ET046778
ET046996
ET046779
ET048061
ET048516
ET046557
ET049561
ET046922
ET046436
ET046554
WRKY_92 [alias=NtWRKY92] ET042371
ET047417
ET051206
ET051396
ET045532
ET043801
ET045704
ET051207
ET041667
ET046975
ET048638
ET048411
ET045400
WRKY_93 [alias=NtWRKY93] ET047744
ET045968
ET051369
ET050503
ET050660
ET048281
ET042596
ET051327
ET050352
ET050914
ET051097
ET050721
ET051370
WRKY_94 [alias=NtWRKY94] ET043821
WRKY_95 [alias=NtWRKY95] ET044942
WRKY_96 [alias=NtWRKY96] ET050942
WRKY_97 [alias=NtWRKY97] ET046274
WRKY_98 [alias=NtWRKY98] ET047959
WRKY_99 [alias=NtWRKY99] ET047702
WRKY_100 [alias=NtWRKY100] ET047958
WRKY_101 [alias=NtWRKY101] ET050205
WRKY_102 [alias=NtWRKY102] ET048092
WRKY_103 [alias=NtWRKY103] ET047876
WRKY_104 [alias=NtWRKY104] ET046543
WRKY_105 [alias=NtWRKY105] ET051575
WRKY_106 [alias=NtWRKY106] ET048091
WRKY_107 [alias=NtWRKY107] ET046972
WRKY_108 [alias=NtWRKY108] ET049742
WRKY_109 [alias=NtWRKY109] ET044060
WRKY_110 [alias=NtWRKY110] ET050874
WRKY_111 [alias=NtWRKY111] ET048794
WRKY_112 [alias=NtWRKY112] ET043633
WRKY_113 [alias=NtWRKY113] ET044464


Tobacco published genes related to transcription factor family WRKY
Family Genbank ID Name
WRKY DQ460475 WRKY12
WRKY AJ871281 WRKY11
WRKY AJ871280 WRKY10
WRKY AB063576 NtWRKY-9
WRKY AB063575 NtWRKY-8
WRKY AB063574 NtWRKY-7
WRKY AB063573 NtWRKY-6
WRKY AB026890 NtWRKY4
WRKY AB022693 NtWRKY1
WRKY AB020590 NtWRKY2
WRKY AY220477 ACRE126
WRKY AB041520 NtEIG-D48
WRKY AX700945 117 (Patent WO03012096)
WRKY AB028022 wizz
WRKY AF193771 WRKY4
WRKY AF193770 WRKY3
WRKY AB024510 TMV response-related gene
WRKY AB020023 NtWRKY3
WRKY AF096299 WRKY2
WRKY AF096298 WRKY1
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