TCP Genomic sequences

Minimum number of tobacco TCP genes: 43

Count of tobacco TCP sequences: 46

Pfam accession: TCP

SHOULD possess TCP domain

The TCP domain is a plant-specific DNA binding domain found in proteins from a diverse array of species, including the cycloidea (cyc) and teosinte branched1 (tb1) gene products and the PCF1 and PCF2 proteins. To understand the role in transcriptional regulation of proteins with this domain, we have analysed the DNA binding and dimerization specificity of the TCP protein family using rice PCF proteins, and further evaluated potential targets for the TCP protein. The seven PCF members including five newly isolated proteins, were able to be grouped into two classes, I and II, based on sequence similarity in the TCP domain. Random binding site selection experiments and electrophoretic mobility shift assays (EMSAs) revealed the consensus DNA binding sequences of these two classes to be distinct but overlapping; GGNCCCAC for class I and GTGGNCCC for class II. The TB1 protein from maize, which belongs to class II, had the same specificity as the rice class II proteins, suggesting the conservation of binding specificity between TCP domains from different species. The yeast 2-hybrid assay and EMSA revealed that these proteins tend to form a homodimer or a heterodimer between members of the same class. We searched predicted 5' flanking sequences of Arabidopsis genes for the consensus binding sequences and found that the consensus sites are distributed in the genome at a considerably lower frequency. We further analysed eight promoters containing the class I consensus TCP sites. The transcriptional activities of six promoters were decreased by a mutation of the TCP binding site, which is consistent with the observation that the class I TCP site can confer transactivation function on a heterologous promoter. These results suggest that the two classes of TCP protein are distinct in DNA binding specificity and transcriptional regulation.

Papers

Cubas, P; Lauter, N; Doebley, J; Coen, E. The TCP domain: a motif found in proteins regulating plant growth and development. Plant J. 1999. 18(2):215-22 PMID: 10363373

Kosugi, S; Ohashi, Y. DNA binding and dimerization specificity and potential targets for the TCP protein family. Plant J. 2002. 30(3):337-48 PMID: 12000681

Reeves, PA; Olmstead, RG. Evolution of the TCP gene family in Asteridae: cladistic and network approaches to understanding regulatory gene family diversification and its impact on morphological evolution. Mol. Biol. Evol. 2003. 20(12):1997-2009 PMID: 12885953



Number of contigs: 44

Number of singlets: 4

Number of N terminal – 3

Number of C terminal – 4

Number of full – 39

Total minimum number – 43




Search sequences and info


Transcription factor sequences
Locus
Description
NCBI
TCP_1 [comment=full] ET047344
ET050197
TCP_2 [comment=full] ET044181
ET046359
TCP_3 [comment=full] ET042002
ET045893
TCP_4 [comment=full TCP protein [Nicotiana sylvestris]] ET047204
ET047205
TCP_5 [comment=C terminal] ET047289
ET043937
TCP_6 [comment=C terminal TCP protein [Nicotiana sylvestris] different than 4] ET042648
ET048744
TCP_7 [comment=full] ET049005
ET049543
TCP_8 [comment=full] ET049839
ET047441
TCP_9 [comment=N terminal] ET050264
ET049387
TCP_10 [comment=full] ET047574
ET047573
ET043600
TCP_11 [comment=full] ET049531
ET050207
ET049915
TCP_12 [comment=full] ET049068
ET044730
ET049781
TCP_13 [comment=full] ET042071
ET045580
ET042070
TCP_14 [comment=full] ET044134
ET043719
ET046160
TCP_15 [comment=full] ET047575
ET050610
ET043063
TCP_16 [comment=full] ET049733
ET050991
ET051049
TCP_17 [comment=full] ET046602
ET046603
ET045743
TCP_18 [comment=N terminal] ET051698
ET046650
ET045560
TCP_19 [comment=full] ET044036
ET050383
ET050152
ET049128
TCP_20 [comment=full] ET050324
ET045234
ET051365
ET044282
TCP_21 [comment=full] ET046539
ET045510
ET046243
ET050338
TCP_22 [comment=full] ET046859
ET046858
ET045746
ET047737
TCP_23 [comment=full] ET049934
ET041733
ET041732
ET049931
TCP_24 [comment=full] ET051450
ET045825
ET043316
ET047988
TCP_25 [comment=full] ET051142
ET051141
ET046615
ET047245
TCP_26 [comment=full] ET044008
ET047640
ET043943
ET044009
TCP_27 [comment=full] ET043905
ET045256
ET049748
ET045664
TCP_28 [comment=full] ET042955
ET043888
ET046905
ET051793
TCP_29 [comment=full] ET049728
ET047535
ET043042
ET049967
ET049727
TCP_30 [comment=full] ET048320
ET043820
ET046651
ET045124
ET044840
TCP_31 [comment=full] ET042057
ET042056
ET051422
ET048789
ET046638
TCP_32 [comment=full] ET049912
ET049930
ET050431
ET043568
ET049327
TCP_33 [comment=full] ET048347
ET045456
ET047850
ET051646
ET047957
TCP_34 [comment=N terminal] ET046394
ET051670
ET044085
ET046395
ET047444
TCP_35 [comment=full] ET047930
ET045069
ET047929
ET042246
ET045068
TCP_36 [comment=full] ET050396
ET050795
ET048388
ET043733
ET047889
TCP_37 [comment=full] ET051240
ET044681
ET046008
ET051122
ET051123
ET051121
TCP_38 [comment=full] ET050456
ET050348
ET042168
ET050815
ET048646
ET050691
ET042512
TCP_39 [comment=full] ET051010
ET051009
ET051011
ET043880
ET044497
ET044796
ET051333
TCP_40 [comment=full] ET050923
ET044378
ET044556
ET042187
ET045340
ET050026
ET050924
TCP_41 [comment=full] ET048816
ET048715
ET050347
ET051635
ET043284
ET042067
ET046334
TCP_42 [comment=full] ET044719
ET050267
ET045027
ET050485
ET044718
ET051712
ET046108
TCP_43 [comment=full] ET043613
ET041666
ET051507
ET044564
ET043374
ET044919
ET043020
ET043054
TCP_44 [comment=full] ET050018
ET050270
ET044471
ET044374
ET044083
ET046742
ET046741
ET046743
ET045171
ET044373
ET043226
TCP_45 [comment=C terminal] ET043623
TCP_46 [comment=C terminal] ET048830


Tobacco published genes related to transcription factor family TCP
Family Genbank ID Name
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