PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

PlantRegMap/PlantTFDB v5.0

Plant Transcription Factor Database

Transcription Factor Information

Basic Information | Signature Domain | Sequence |

Basic Information? help Back to Top

TF ID

AT3G15030.2

Common Name

K15M2.17, MEE35, TCP4

Organism

Arabidopsis thaliana

Taxonomic ID

3702

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis

Family

TCP

Protein Properties

Length: 420aa MW: 45963.4 Da PI: 7.2936

Description

TCP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT3G15030.2	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	TCP	121	1.4e-37	43	213	2	120
TCP 2 agkkdrhskihTkvggRdRRvRlsaecaarfFdLqdeLGfdkdsktieWLlqqakpaikeltgt........................ssssasecea 75 +g+kdrhsk++T++g+RdRRvRlsa++a++f+d+qd+LGfd++sk+++WL+++ak++i+el+++ +++s+s + AT3G15030.2 43 TGRKDRHSKVCTAKGPRDRRVRLSAHTAIQFYDVQDRLGFDRPSKAVDWLIKKAKTSIDELAELppwnpadairlaaanakprrttakTQISPSPPPP 140 79**************************************************************9999999999988888887766652222222233 PP TCP 76 esssssas.........nsssg........................kaaksaakskksqksaasalnlakesrakara 120 ++++++++ g ++ + +++++++++ +nl+++ +++ AT3G15030.2 141 QQQQQQQQlqfgvgfngG---GaehpsnnessflppsmdsdsiadtIKSFFPVIGSSTEAPSN--HNLMHNYHHQHPP 213 333333333344444440...044444445667777777777776644444444444444444..5555555544444 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF03634	2.6E-32	43	147	IPR005333	Transcription factor, TCP
PROSITE profile	PS51369	34.016	45	103	IPR017887	Transcription factor TCP subgroup

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0009793	Biological Process	embryo development ending in seed dormancy
GO:0009965	Biological Process	leaf morphogenesis
GO:0030154	Biological Process	cell differentiation
GO:0045962	Biological Process	positive regulation of development, heterochronic
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0005515	Molecular Function	protein binding

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0000013	anatomy	cauline leaf
PO:0000037	anatomy	shoot apex
PO:0000056	anatomy	flower bud
PO:0000293	anatomy	guard cell
PO:0008019	anatomy	leaf lamina base
PO:0009001	anatomy	fruit
PO:0009005	anatomy	root
PO:0009006	anatomy	shoot system
PO:0009009	anatomy	plant embryo
PO:0009010	anatomy	seed
PO:0009025	anatomy	vascular leaf
PO:0009029	anatomy	stamen
PO:0009030	anatomy	carpel
PO:0009031	anatomy	sepal
PO:0009032	anatomy	petal
PO:0009046	anatomy	flower
PO:0009047	anatomy	stem
PO:0020030	anatomy	cotyledon
PO:0020038	anatomy	petiole
PO:0025022	anatomy	collective leaf structure
PO:0001054	developmental stage	vascular leaf senescent stage
PO:0001078	developmental stage	plant embryo cotyledonary stage
PO:0001081	developmental stage	mature plant embryo stage
PO:0004507	developmental stage	plant embryo bilateral stage
PO:0007064	developmental stage	LP.12 twelve leaves visible stage
PO:0007095	developmental stage	LP.08 eight leaves visible stage
PO:0007098	developmental stage	LP.02 two leaves visible stage
PO:0007103	developmental stage	LP.10 ten leaves visible stage
PO:0007115	developmental stage	LP.04 four leaves visible stage
PO:0007123	developmental stage	LP.06 six leaves visible stage
PO:0007611	developmental stage	petal differentiation and expansion stage
PO:0007616	developmental stage	flowering stage

Sequence ? help Back to Top
Protein Sequence Length: 420 aa Download sequence Send to blast
MSDDQFHHPP PPSSMRHRST SDAADGGCGE IVEVQGGHIV RSTGRKDRHS KVCTAKGPRD 60 RRVRLSAHTA IQFYDVQDRL GFDRPSKAVD WLIKKAKTSI DELAELPPWN PADAIRLAAA 120 NAKPRRTTAK TQISPSPPPP QQQQQQQQLQ FGVGFNGGGA EHPSNNESSF LPPSMDSDSI 180 ADTIKSFFPV IGSSTEAPSN HNLMHNYHHQ HPPDLLSRTN SQNQDLRLSL QSFPDGPPSL 240 LHHQHHHHTS ASASEPTLFY GQSNPLGFDT SSWEQQSSEF GRIQRLVAWN SGGGGGATDT 300 GNGGGFLFAP PTPSTTSFQP VLGQSQQLYS QRGPLQSSYS PMIRAWFDPH HHHQSISTDD 360 LNHHHHLPPP VHQSAIPGIG FASGEFSSGF RIPARFQGQE EEQHDGLTHK PSSASSISRH

Sequence ? help Back to Top

Protein Sequence Length: 420 aa Download sequence Send to blast

MSDDQFHHPP PPSSMRHRST SDAADGGCGE IVEVQGGHIV RSTGRKDRHS KVCTAKGPRD  60
RRVRLSAHTA IQFYDVQDRL GFDRPSKAVD WLIKKAKTSI DELAELPPWN PADAIRLAAA  120
NAKPRRTTAK TQISPSPPPP QQQQQQQQLQ FGVGFNGGGA EHPSNNESSF LPPSMDSDSI  180
ADTIKSFFPV IGSSTEAPSN HNLMHNYHHQ HPPDLLSRTN SQNQDLRLSL QSFPDGPPSL  240
LHHQHHHHTS ASASEPTLFY GQSNPLGFDT SSWEQQSSEF GRIQRLVAWN SGGGGGATDT  300
GNGGGFLFAP PTPSTTSFQP VLGQSQQLYS QRGPLQSSYS PMIRAWFDPH HHHQSISTDD  360
LNHHHHLPPP VHQSAIPGIG FASGEFSSGF RIPARFQGQE EEQHDGLTHK PSSASSISRH

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5zkt_A	4e-20	50	103	1	54	Putative transcription factor PCF6
5zkt_B	4e-20	50	103	1	54	Putative transcription factor PCF6
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
At.23764	0.0	floral meristem\| seed

Expression -- Microarray ? help Back to Top
Source	ID	E-value
GEO	334185358	0.0
Genevisible	257267_at	0.0
Expression Atlas	AT3G15030	-
AtGenExpress	AT3G15030	-
ATTED-II	AT3G15030	-

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Expressed in cotyledons during embryogenesis. Expressed during ovule development (PubMed:25378179). {ECO:0000269\|PubMed:25378179}.
Uniprot	TISSUE SPECIFICITY: Expressed in cotyledons, particularly in the vascular region, in leaves, roots, buds, flowers and immature siliques. {ECO:0000269\|PubMed:17307931}.

Functional Description ? help Back to Top
Source	Description
TAIR	Arabidopsis thaliana TCP family transcription factor. Regulated by miR319. Involved in heterchronic regulation of leaf differentiation.
UniProt	Transcription factor playing a pivotal role in the control of morphogenesis of shoot organs by negatively regulating the expression of boundary-specific genes such as CUC genes, probably through the induction of miRNA (e.g. miR164) (PubMed:12931144, PubMed:17307931). Required during early steps of embryogenesis (PubMed:15634699). Participates in ovule develpment (PubMed:25378179). Activates LOX2 expression by binding to the 5'-GGACCA-3' motif found in its promoter (PubMed:18816164). {ECO:0000269\|PubMed:12931144, ECO:0000269\|PubMed:15634699, ECO:0000269\|PubMed:17307931, ECO:0000269\|PubMed:18816164, ECO:0000269\|PubMed:25378179}.

Function -- GeneRIF ? help Back to Top
a miRNA-resistant version of TCP4, when expressed in petals and stamens, causes these organs not to develop [PMID: 20007771] Arabidopsis plants with an increased activity of the transcription factor TCP4, which reduces cell proliferation in leaves, have higher miR396 and lower GRF levels. [PMID: 20023165] hyper-activation of TCP4 revealed its role in determining the timing of crucial developmental events, both at the organ and organism level. [PMID: 21518050] TCP4 protein blocks cell cycle of budding yeast, specifically at G1->S transition, by regulating G1 checkpoint control pathway. [PMID: 21658370] These analyses indicate a role for auxin, gibberellic acid and abscisic acid in TCP4-mediated control of leaf growth. [PMID: 21904111] Data show that the expression of TCP4 and IAMT1 that encodes a methyltransferase converting free indole-3-acetic acid (IAA) to methyl-IAA ester (MeIAA) was induced and the induction level was dependent on the abundance of TaWRKY71-1 transcripts. [PMID: 23671653] A small increase in TCP4 activity has an immediate impact on leaf cell number, by significantly reducing cell proliferation through miR319. [PMID: 25053833] Data showed that SPOROCYTELESS (SPL) most likely functions as a transcription repressor by interacting with TCP family transcription factors and the TOPLESS (TPL) co-repressors. [PMID: 25527103] miR319 and its target TCP4 can act as switches that turn on secondary cell wall synthesis and programmed cell death. [PMID: 28233945] Our yeast one-hybrid analysis revealed that class II CIN-TCPs, including TCP4, bind to the CO promoter. TCP4 induces CO expression around dusk by directly associating with the CO promoter in vivo. In addition, TCP4 binds to another flowering regulator, GIGANTEA (GI), in the nucleus, and induces CO expression in a GI-dependent manner [PMID: 28628608] Mutations in MIR319 and gain-of-function mutations in the TCP4 gene conferred resistance against miR319 and impaired the cotyledon boundary and leaf serration formation. Taken together, these findings demonstrate that the MIR319 and TCP gene families underlie robust and multilayer control of leaf development. [PMID: 28842549] Detailed genetic analyses show that GIS and TCP4 work in same pathway and GIS function is required for TCP4-mediated regulation of trichome differentiation. [PMID: 29165850] We induced a microRNA-resistant form of TCP4 at various developmental stages of leaf primordium that lacked the activity of TCP4 and its homologues and followed its effect on growth kinematics. By combining this with spatio-temporal gene expression analysis, we show that TCP4 commits leaf cells within the transition zone to exit proliferation and enter differentiation. [PMID: 30742619]

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00062	PBM	25215497	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT3G15030.2

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Repressed by the miRNA miR-JAW/miR319 (PubMed:12931144, PubMed:18816164). {ECO:0000269\|PubMed:12931144, ECO:0000269\|PubMed:18816164}.

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	Retrieve

Interaction ? help Back to Top
Source	Intact With
BioGRID	AT3G02150, AT3G27010, AT3G47620, AT4G18390, AT4G27330, AT5G08070, AT5G08330, AT5G51910, AT5G60970, AT1G30210, AT1G35560, AT1G53230, AT1G58100, AT1G65620, AT1G69690

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT3G15030

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AK316704	0.0	AK316704.1 Arabidopsis thaliana AT3G15030 mRNA, complete cds, clone: RAFL06-89-F15.
GenBank	AP000370	0.0	AP000370.1 Arabidopsis thaliana genomic DNA, chromosome 3, TAC clone:K15M2.
GenBank	AY094444	0.0	AY094444.1 Arabidopsis thaliana AT3g15030/K15M2_17 mRNA, complete cds.
GenBank	AY149957	0.0	AY149957.1 Arabidopsis thaliana At3g15030/K15M2_17 mRNA, complete cds.
GenBank	CP002686	0.0	CP002686.1 Arabidopsis thaliana chromosome 3, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_001189896.1	0.0	TCP family transcription factor 4
Refseq	NP_001319557.1	0.0	TCP family transcription factor 4
Refseq	NP_188121.1	0.0	TCP family transcription factor 4
Refseq	NP_850589.1	0.0	TCP family transcription factor 4
Swissprot	Q8LPR5	0.0	TCP4_ARATH; Transcription factor TCP4
TrEMBL	A0A384KY84	0.0	A0A384KY84_ARATH; TCP4
TrEMBL	B9DFB4	0.0	B9DFB4_ARATH; AT3G15030 protein
STRING	AT3G15030.1	0.0	(Arabidopsis thaliana)

Link Out ? help Back to Top
Phytozome	AT3G15030.2
Entrez Gene	820732
iHOP	AT3G15030
wikigenes	AT3G15030

Publications ? help Back to Top
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): p. 215-22 [PMID:10363373] Riechmann JL, et al. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science, 2000. 290(5499): p. 2105-10 [PMID:11118137] Palatnik JF, et al. Control of leaf morphogenesis by microRNAs. Nature, 2003. 425(6955): p. 257-63 [PMID:12931144] Yamada K, et al. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science, 2003. 302(5646): p. 842-6 [PMID:14593172] Souret FF,Kastenmayer JP,Green PJ AtXRN4 degrades mRNA in Arabidopsis and its substrates include selected miRNA targets. Mol. Cell, 2004. 15(2): p. 173-83 [PMID:15260969] Pagnussat GC, et al. Genetic and molecular identification of genes required for female gametophyte development and function in Arabidopsis. Development, 2005. 132(3): p. 603-14 [PMID:15634699] Qin G, et al. An indole-3-acetic acid carboxyl methyltransferase regulates Arabidopsis leaf development. Plant Cell, 2005. 17(10): p. 2693-704 [PMID:16169896] Aguilar-Martínez JA,Poza-Carrión C,Cubas P Arabidopsis BRANCHED1 acts as an integrator of branching signals within axillary buds. Plant Cell, 2007. 19(2): p. 458-72 [PMID:17307924] Koyama T,Furutani M,Tasaka M,Ohme-Takagi M TCP transcription factors control the morphology of shoot lateral organs via negative regulation of the expression of boundary-specific genes in Arabidopsis. Plant Cell, 2007. 19(2): p. 473-84 [PMID:17307931] Ascencio-Ib Global analysis of Arabidopsis gene expression uncovers a complex array of changes impacting pathogen response and cell cycle during geminivirus infection. Plant Physiol., 2008. 148(1): p. 436-54 [PMID:18650403] Efroni I,Blum E,Goldshmidt A,Eshed Y A protracted and dynamic maturation schedule underlies Arabidopsis leaf development. Plant Cell, 2008. 20(9): p. 2293-306 [PMID:18805992] Schommer C, et al. Control of jasmonate biosynthesis and senescence by miR319 targets. PLoS Biol., 2008. 6(9): p. e230 [PMID:18816164] Nag A,King S,Jack T miR319a targeting of TCP4 is critical for petal growth and development in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A., 2009. 106(52): p. 22534-9 [PMID:20007771] Rodriguez RE, et al. Control of cell proliferation in Arabidopsis thaliana by microRNA miR396. Development, 2010. 137(1): p. 103-12 [PMID:20023165] Aggarwal P, et al. Identification of specific DNA binding residues in the TCP family of transcription factors in Arabidopsis. Plant Cell, 2010. 22(4): p. 1174-89 [PMID:20363772] Koyama T,Mitsuda N,Seki M,Shinozaki K,Ohme-Takagi M TCP transcription factors regulate the activities of ASYMMETRIC LEAVES1 and miR164, as well as the auxin response, during differentiation of leaves in Arabidopsis. Plant Cell, 2010. 22(11): p. 3574-88 [PMID:21119060] Sarvepalli K,Nath U Hyper-activation of the TCP4 transcription factor in Arabidopsis thaliana accelerates multiple aspects of plant maturation. Plant J., 2011. 67(4): p. 595-607 [PMID:21518050] Aggarwal P, et al. The TCP4 transcription factor of Arabidopsis blocks cell division in yeast at G1→S transition. Biochem. Biophys. Res. Commun., 2011. 410(2): p. 276-81 [PMID:21658370] Sarvepalli K,Nath U Interaction of TCP4-mediated growth module with phytohormones. Plant Signal Behav, 2011. 6(10): p. 1440-3 [PMID:21904111] Causier B,Ashworth M,Guo W,Davies B The TOPLESS interactome: a framework for gene repression in Arabidopsis. Plant Physiol., 2012. 158(1): p. 423-38 [PMID:22065421] Viola IL,Reinheimer R,Ripoll R,Manassero NG,Gonzalez DH Determinants of the DNA binding specificity of class I and class II TCP transcription factors. J. Biol. Chem., 2012. 287(1): p. 347-56 [PMID:22074922] Li Z,Li B,Shen WH,Huang H,Dong A TCP transcription factors interact with AS2 in the repression of class-I KNOX genes in Arabidopsis thaliana. Plant J., 2012. 71(1): p. 99-107 [PMID:22380849] Yang X, et al. Evolution of double positive autoregulatory feedback loops in CYCLOIDEA2 clade genes is associated with the origin of floral zygomorphy. Plant Cell, 2012. 24(5): p. 1834-47 [PMID:22649271] Mecchia MA,Debernardi JM,Rodriguez RE,Schommer C,Palatnik JF MicroRNA miR396 and RDR6 synergistically regulate leaf development. Mech. Dev., 2013. 130(1): p. 2-13 [PMID:22889666] Efroni I, et al. Regulation of leaf maturation by chromatin-mediated modulation of cytokinin responses. Dev. Cell, 2013. 24(4): p. 438-45 [PMID:23449474] Qin Z, et al. Ectopic expression of a wheat WRKY transcription factor gene TaWRKY71-1 results in hyponastic leaves in Arabidopsis thaliana. PLoS ONE, 2013. 8(5): p. e63033 [PMID:23671653] Danisman S, et al. Analysis of functional redundancies within the Arabidopsis TCP transcription factor family. J. Exp. Bot., 2013. 64(18): p. 5673-85 [PMID:24129704] Zhao J,Favero DS,Peng H,Neff MM Arabidopsis thaliana AHL family modulates hypocotyl growth redundantly by interacting with each other via the PPC/DUF296 domain. Proc. Natl. Acad. Sci. U.S.A., 2013. 110(48): p. E4688-97 [PMID:24218605] Schommer C,Debernardi JM,Bresso EG,Rodriguez RE,Palatnik JF Repression of cell proliferation by miR319-regulated TCP4. Mol Plant, 2014. 7(10): p. 1533-44 [PMID:25053833] Wei B, et al. The molecular mechanism of sporocyteless/nozzle in controlling Arabidopsis ovule development. Cell Res., 2015. 25(1): p. 121-34 [PMID:25378179] Chen GH,Sun JY,Liu M,Liu J,Yang WC SPOROCYTELESS is a novel embryophyte-specific transcription repressor that interacts with TPL and TCP proteins in Arabidopsis. J Genet Genomics, 2014. 41(12): p. 617-25 [PMID:25527103] Ju Y, et al. Arabidopsis JINGUBANG Is a Negative Regulator of Pollen Germination That Prevents Pollination in Moist Environments. Plant Cell, 2016. 28(9): p. 2131-2146 [PMID:27468890] Challa KR,Aggarwal P,Nath U Activation of YUCCA5 by the Transcription Factor TCP4 Integrates Developmental and Environmental Signals to Promote Hypocotyl Elongation in Arabidopsis. Plant Cell, 2016. 28(9): p. 2117-2130 [PMID:27597774] Alvarez JP,Furumizu C,Efroni I,Eshed Y,Bowman JL Active suppression of a leaf meristem orchestrates determinate leaf growth. Elife, 2017. [PMID:27710768] Li J, et al. RABBIT EARS regulates the transcription of TCP4 during petal development in Arabidopsis. J. Exp. Bot., 2016. 67(22): p. 6473-6480 [PMID:27838638] Sun X, et al. Activation of secondary cell wall biosynthesis by miR319-targeted TCP4 transcription factor. Plant Biotechnol. J., 2017. 15(10): p. 1284-1294 [PMID:28233945] Kubota A, et al. TCP4-dependent induction of CONSTANS transcription requires GIGANTEA in photoperiodic flowering in Arabidopsis. PLoS Genet., 2017. 13(6): p. e1006856 [PMID:28628608] Koyama T,Sato F,Ohme-Takagi M Roles of miR319 and TCP Transcription Factors in Leaf Development. Plant Physiol., 2017. 175(2): p. 874-885 [PMID:28842549] Bresso EG,Chorostecki U,Rodriguez RE,Palatnik JF,Schommer C Spatial Control of Gene Expression by miR319-Regulated TCP Transcription Factors in Leaf Development. Plant Physiol., 2018. 176(2): p. 1694-1708 [PMID:29133375] Vadde BVL,Challa KR,Nath U The TCP4 transcription factor regulates trichome cell differentiation by directly activating GLABROUS INFLORESCENCE STEMS in Arabidopsis thaliana. Plant J., 2018. 93(2): p. 259-269 [PMID:29165850] Challa KR,Rath M,Nath U The CIN-TCP transcription factors promote commitment to differentiation in Arabidopsis leaf pavement cells via both auxin-dependent and independent pathways. PLoS Genet., 2019. 15(2): p. e1007988 [PMID:30742619]