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

AT3G20840.1

Common Name

AIL3, MOE17.15, PLT1

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

AP2

Protein Properties

Length: 574aa MW: 62875.5 Da PI: 6.3596

Description

AP2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT3G20840.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	AP2	42.9	1.2e-13	180	239	1	55
AP2 1 sgykGVrwdkkrgrWvAeIrd.pse.ng..kr.krfslgkfgtaeeAakaaiaarkkleg 55 s y+GV++++++gr++A+++d + g ++ ++++lg ++ +++Aa+ ++ a++k++g AT3G20840.1 180 SIYRGVTRHRWTGRYEAHLWDnSCRrEGqsRKgRQVYLGGYDKEDKAARSYDLAALKYWG 239 57*****************666664477446******99***********98 PP
2	AP2	47	6.3e-15	284	333	3	55
AP2 3 ykGVrwdkkrgrWvAeIrdpsengkrkrfslgkfgtaeeAakaaiaarkkleg 55 y+GV+++++ grW A+I + +k +lg+f t+eeAa+a++ a+ k++g AT3G20840.1 284 YRGVTRHHQHGRWQARIGRVAG---NKDLYLGTFSTEEEAAEAYDIAAIKFRG 333 9*************988532...5**********************998 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF00847	7.2E-11	180	239	IPR001471	AP2/ERF domain
CDD	cd00018	8.46E-21	180	249	No hit	No description
SuperFamily	SSF54171	9.15E-16	180	248	IPR016177	DNA-binding domain
SMART	SM00380	2.9E-28	181	253	IPR001471	AP2/ERF domain
PROSITE profile	PS51032	18.716	181	247	IPR001471	AP2/ERF domain
Gene3D	G3DSA:3.30.730.10	2.4E-14	181	247	IPR001471	AP2/ERF domain
PRINTS	PR00367	5.2E-6	182	193	IPR001471	AP2/ERF domain
SuperFamily	SSF54171	9.15E-18	282	342	IPR016177	DNA-binding domain
CDD	cd00018	2.40E-24	282	343	No hit	No description
SMART	SM00380	1.5E-32	283	347	IPR001471	AP2/ERF domain
Gene3D	G3DSA:3.30.730.10	4.8E-18	283	341	IPR001471	AP2/ERF domain
PROSITE profile	PS51032	19.506	283	341	IPR001471	AP2/ERF domain
Pfam	PF00847	1.5E-9	284	333	IPR001471	AP2/ERF domain
PRINTS	PR00367	5.2E-6	323	343	IPR001471	AP2/ERF domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0000723	Biological Process	telomere maintenance
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0007389	Biological Process	pattern specification process
GO:0009734	Biological Process	auxin-activated signaling pathway
GO:0009873	Biological Process	ethylene-activated signaling pathway
GO:0010449	Biological Process	root meristem growth
GO:0019827	Biological Process	stem cell population maintenance
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0009005	anatomy	root

Sequence ? help Back to Top
Protein Sequence Length: 574 aa Download sequence Send to blast
MNSNNWLGFP LSPNNSSLPP HEYNLGLVSD HMDNPFQTQE WNMINPHGGG GDEGGEVPKV 60 ADFLGVSKPD ENQSNHLVAY NDSDYYFHTN SLMPSVQSND VVVAACDSNT PNNSSYHELQ 120 ESAHNLQSLT LSMGTTAGNN VVDKASPSET TGDNASGGAL AVVETATPRR ALDTFGQRTS 180 IYRGVTRHRW TGRYEAHLWD NSCRREGQSR KGRQVYLGGY DKEDKAARSY DLAALKYWGP 240 STTTNFPITN YEKEVEEMKH MTRQEFVAAI RRKSSGFSRG ASMYRGVTRH HQHGRWQARI 300 GRVAGNKDLY LGTFSTEEEA AEAYDIAAIK FRGLNAVTNF EINRYDVKAI LESSTLPIGG 360 GAAKRLKEAQ ALESSRKREA EMIALGSSFQ YGGGSSTGSG STSSRLQLQP YPLSIQQPLE 420 PFLSLQNNDI SHYNNNNAHD SSSFNHHSYI QTQLHLHQQT NNYLQQQSSQ NSQQLYNAYL 480 HSNPALLHGL VSTSIVDNNN NNGGSSGSYN TAAFLGNHGI GIGSSSTVGS TEEFPTVKTD 540 YDMPSSDGTG GYSGWTSESV QGSNPGGVFT MWNE

Sequence ? help Back to Top

Protein Sequence Length: 574 aa Download sequence Send to blast

MNSNNWLGFP LSPNNSSLPP HEYNLGLVSD HMDNPFQTQE WNMINPHGGG GDEGGEVPKV  60
ADFLGVSKPD ENQSNHLVAY NDSDYYFHTN SLMPSVQSND VVVAACDSNT PNNSSYHELQ  120
ESAHNLQSLT LSMGTTAGNN VVDKASPSET TGDNASGGAL AVVETATPRR ALDTFGQRTS  180
IYRGVTRHRW TGRYEAHLWD NSCRREGQSR KGRQVYLGGY DKEDKAARSY DLAALKYWGP  240
STTTNFPITN YEKEVEEMKH MTRQEFVAAI RRKSSGFSRG ASMYRGVTRH HQHGRWQARI  300
GRVAGNKDLY LGTFSTEEEA AEAYDIAAIK FRGLNAVTNF EINRYDVKAI LESSTLPIGG  360
GAAKRLKEAQ ALESSRKREA EMIALGSSFQ YGGGSSTGSG STSSRLQLQP YPLSIQQPLE  420
PFLSLQNNDI SHYNNNNAHD SSSFNHHSYI QTQLHLHQQT NNYLQQQSSQ NSQQLYNAYL  480
HSNPALLHGL VSTSIVDNNN NNGGSSGSYN TAAFLGNHGI GIGSSSTVGS TEEFPTVKTD  540
YDMPSSDGTG GYSGWTSESV QGSNPGGVFT MWNE

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
At.38171	0.0	seed

Expression -- Microarray ? help Back to Top
Source	ID	E-value
GEO	79409850	0.0
Genevisible	257976_at	0.0
Expression Atlas	AT3G20840	-
AtGenExpress	AT3G20840	-
ATTED-II	AT3G20840	-

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Accumulates in the basal embryo region that gives rise to hypocotyl, root, and root stem cells. Expressed in the root meristem throughout embryo development. {ECO:0000269\|PubMed:15454085, ECO:0000269\|PubMed:20190735}.
Uniprot	TISSUE SPECIFICITY: Expressed in roots, seedlings, flowers, and siliques. Also detected at low levels in leaves. In roots, specifically detected in the distal root meristem, including the QC. This tissue specificity is regulated by auxin gradient and depends on PIN proteins. {ECO:0000269\|PubMed:15454085, ECO:0000269\|PubMed:15635403, ECO:0000269\|PubMed:15988559, ECO:0000269\|PubMed:16424342, ECO:0000269\|PubMed:20190735}.

Functional Description ? help Back to Top
Source	Description
TAIR	Encodes a member of the AINTEGUMENTA-like (AIL) subclass of the AP2/EREBP family of transcription factors and is essential for quiescent center (QC) specification and stem cell activity. It is a key effector for establishment of the stem cell niche during embryonic pattern formation. It is transcribed in response to auxin accumulation and is dependent on auxin response transcription factors.
UniProt	Probably acts as a transcriptional activator. Binds to the GCC-box pathogenesis-related promoter element. May be involved in the regulation of gene expression by stress factors and by components of stress signal transduction pathways (By similarity). Master regulator of basal/root fate. Essential for root quiescent center (QC) and columella specification, stem cell activity, as well as for establishment of the stem cell niche during embryogenesis. Modulates the root polar auxin transport by regulating the distribution of PIN genes. Essential role in respecifying pattern and polarity in damaged roots. Direct target of the transcriptional corepressor TPL. Expression levels and patterns regulated post-transcriptionally by root meristem growth factors (RGFs). {ECO:0000250, ECO:0000269\|PubMed:15454085, ECO:0000269\|PubMed:15635403, ECO:0000269\|PubMed:16424342, ECO:0000269\|PubMed:20190735}.

Function -- GeneRIF ? help Back to Top
RopGEF7 is required for root meristem maintenance as it regulates the expression of PLETHORA1 (PLT1) and PLT2, which are key transcription factors that mediate the patterning of the root stem cell niche. [PMID: 21828289] PLT1 and PLT2 are key interaction nodes between jasmonate and auxin in the regulation of root stem cell niche maintenance and meristem activity. [PMID: 21954460] These results suggest that endogenous L-cysteine level acts to maintain root stem cell niche by regulating basal- and auxin-induced expression of PLT1/2 and SCR/SHR. [PMID: 24798139] The abo8 mutation affects the expression of PLT1 and PLT2; plt1 and plt2 mutants are sensitive to ABA in root growth [PMID: 25522358] ABA treatment reduced the expression levels of the PIN-FORMEDs (PIN) auxin efflux carriers, PIN1, PIN3, PIN4, and PIN7, to a greater extent in the root meristems of arf2-101 mutant than in the wild type. ARF2 positively mediates the transcripts of transcription factor PLETHORA 1 (PLT1) gene but negatively mediates PLT2 at protein level in root meristems. [PMID: 28074634]

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00368	DAP	27203113	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT3G20840.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By auxin accumulation. {ECO:0000269\|PubMed:15454085}.

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

Regulation -- ATRM (Manually Curated Upstream Regulators) ? help Back to Top
Source	Upstream Regulator (A: Activate/R: Repress)
ATRM	AT1G19850 (A), AT5G20730 (A)

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT3G20840

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AY506549	0.0	AY506549.1 Arabidopsis thaliana PLETHORA1 (PLT1) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_188720.2	0.0	Integrase-type DNA-binding superfamily protein
Swissprot	Q5YGP8	0.0	PLET1_ARATH; AP2-like ethylene-responsive transcription factor PLT1
TrEMBL	D7KZX2	0.0	D7KZX2_ARALL; Uncharacterized protein
STRING	AT3G20840.1	0.0	(Arabidopsis thaliana)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM3015	27	67
Representative plant	OGRP112	17	209

Link Out ? help Back to Top
Phytozome	AT3G20840.1
Entrez Gene	821632
iHOP	AT3G20840
wikigenes	AT3G20840

Publications ? help Back to Top
Riechmann JL, et al. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science, 2000. 290(5499): p. 2105-10 [PMID:11118137] Aida M, et al. The PLETHORA genes mediate patterning of the Arabidopsis root stem cell niche. Cell, 2004. 119(1): p. 109-20 [PMID:15454085] Blilou I, et al. The PIN auxin efflux facilitator network controls growth and patterning in Arabidopsis roots. Nature, 2005. 433(7021): p. 39-44 [PMID:15635403] Nole-Wilson S,Tranby TL,Krizek BA AINTEGUMENTA-like (AIL) genes are expressed in young tissues and may specify meristematic or division-competent states. Plant Mol. Biol., 2005. 57(5): p. 613-28 [PMID:15988559] Wang JW, et al. Control of root cap formation by MicroRNA-targeted auxin response factors in Arabidopsis. Plant Cell, 2005. 17(8): p. 2204-16 [PMID:16006581] Duarte JM, et al. Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis. Mol. Biol. Evol., 2006. 23(2): p. 469-78 [PMID:16280546] Nakano T,Suzuki K,Fujimura T,Shinshi H Genome-wide analysis of the ERF gene family in Arabidopsis and rice. Plant Physiol., 2006. 140(2): p. 411-32 [PMID:16407444] Xu J, et al. A molecular framework for plant regeneration. Science, 2006. 311(5759): p. 385-8 [PMID:16424342] Dello Ioio R, et al. Cytokinins determine Arabidopsis root-meristem size by controlling cell differentiation. Curr. Biol., 2007. 17(8): p. 678-82 [PMID:17363254] Galinha C, et al. PLETHORA proteins as dose-dependent master regulators of Arabidopsis root development. Nature, 2007. 449(7165): p. 1053-7 [PMID:17960244] Iyer-Pascuzzi AS,Benfey PN Transcriptional networks in root cell fate specification. Biochim. Biophys. Acta, 2009. 1789(4): p. 315-25 [PMID:18973837] Atta R, et al. Pluripotency of Arabidopsis xylem pericycle underlies shoot regeneration from root and hypocotyl explants grown in vitro. Plant J., 2009. 57(4): p. 626-44 [PMID:18980654] Casson SA,Topping JF,Lindsey K MERISTEM-DEFECTIVE, an RS domain protein, is required for the correct meristem patterning and function in Arabidopsis. Plant J., 2009. 57(5): p. 857-69 [PMID:19000164] Ishida T, et al. SUMO E3 ligase HIGH PLOIDY2 regulates endocycle onset and meristem maintenance in Arabidopsis. Plant Cell, 2009. 21(8): p. 2284-97 [PMID:19666737] Sato A,Yamamoto KT What's the physiological role of domain II-less Aux/IAA proteins? Plant Signal Behav, 2008. 3(7): p. 496-7 [PMID:19704497] Smith ZR,Long JA Control of Arabidopsis apical-basal embryo polarity by antagonistic transcription factors. Nature, 2010. 464(7287): p. 423-6 [PMID:20190735] Ding Z,Friml J Auxin regulates distal stem cell differentiation in Arabidopsis roots. Proc. Natl. Acad. Sci. U.S.A., 2010. 107(26): p. 12046-51 [PMID:20543136] Matsuzaki Y,Ogawa-Ohnishi M,Mori A,Matsubayashi Y Secreted peptide signals required for maintenance of root stem cell niche in Arabidopsis. Science, 2010. 329(5995): p. 1065-7 [PMID:20798316] Zhou W, et al. Arabidopsis Tyrosylprotein sulfotransferase acts in the auxin/PLETHORA pathway in regulating postembryonic maintenance of the root stem cell niche. Plant Cell, 2010. 22(11): p. 3692-709 [PMID:21045165] Chen M, et al. RopGEF7 regulates PLETHORA-dependent maintenance of the root stem cell niche in Arabidopsis. Plant Cell, 2011. 23(8): p. 2880-94 [PMID:21828289] Gu XL,Wang H,Huang H,Cui XF SPT6L encoding a putative WG/GW-repeat protein regulates apical-basal polarity of embryo in Arabidopsis. Mol Plant, 2012. 5(1): p. 249-59 [PMID:21948524] Chen Q, et al. The basic helix-loop-helix transcription factor MYC2 directly represses PLETHORA expression during jasmonate-mediated modulation of the root stem cell niche in Arabidopsis. Plant Cell, 2011. 23(9): p. 3335-52 [PMID:21954460] Feng Z,Sun X,Wang G,Liu H,Zhu J LBD29 regulates the cell cycle progression in response to auxin during lateral root formation in Arabidopsis thaliana. Ann. Bot., 2012. 110(1): p. 1-10 [PMID:22334497] Dhonukshe P, et al. A PLETHORA-auxin transcription module controls cell division plane rotation through MAP65 and CLASP. Cell, 2012. 149(2): p. 383-96 [PMID:22500804] Lee DK,Sieburth LE The bps signal: embryonic arrest from an auxin-independent mechanism in bypass triple mutants. Plant Signal Behav, 2012. 7(6): p. 698-700 [PMID:22580686] Kanei M,Horiguchi G,Tsukaya H Stable establishment of cotyledon identity during embryogenesis in Arabidopsis by ANGUSTIFOLIA3 and HANABA TARANU. Development, 2012. 139(13): p. 2436-46 [PMID:22669825] Peng Y, et al. Control of root meristem size by DA1-RELATED PROTEIN2 in Arabidopsis. Plant Physiol., 2013. 161(3): p. 1542-56 [PMID:23296689] Koizumi K,Gallagher KL Identification of SHRUBBY, a SHORT-ROOT and SCARECROW interacting protein that controls root growth and radial patterning. Development, 2013. 140(6): p. 1292-300 [PMID:23444357] Peng Y, et al. DAR2 acts as an important node connecting cytokinin, auxin, SHY2 and PLT1/2 in root meristem size control. Plant Signal Behav, 2013. 8(6): p. e24226 [PMID:23518585] Hong LW,Yan DW,Liu WC,Chen HG,Lu YT TIME FOR COFFEE controls root meristem size by changes in auxin accumulation in Arabidopsis. J. Exp. Bot., 2014. 65(1): p. 275-86 [PMID:24277277] Tian H,Jia Y,Niu T,Yu Q,Ding Z The key players of the primary root growth and development also function in lateral roots in Arabidopsis. Plant Cell Rep., 2014. 33(5): p. 745-53 [PMID:24504658] Wang Z,Mao JL,Zhao YJ,Li CY,Xiang CB L-Cysteine inhibits root elongation through auxin/PLETHORA and SCR/SHR pathway in Arabidopsis thaliana. J Integr Plant Biol, 2015. 57(2): p. 186-97 [PMID:24798139] Zhao Q, et al. Sulfur nutrient availability regulates root elongation by affecting root indole-3-acetic acid levels and the stem cell niche. J Integr Plant Biol, 2014. 56(12): p. 1151-63 [PMID:24831283] Huang JB, et al. ROP3 GTPase contributes to polar auxin transport and auxin responses and is important for embryogenesis and seedling growth in Arabidopsis. Plant Cell, 2014. 26(9): p. 3501-18 [PMID:25217509] Yang L, et al. ABA-mediated ROS in mitochondria regulate root meristem activity by controlling PLETHORA expression in Arabidopsis. PLoS Genet., 2014. 10(12): p. e1004791 [PMID:25522358] Jin J, et al. An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors. Mol. Biol. Evol., 2015. 32(7): p. 1767-73 [PMID:25750178] Gonz Single-cell telomere-length quantification couples telomere length to meristem activity and stem cell development in Arabidopsis. Cell Rep, 2015. 11(6): p. 977-89 [PMID:25937286] Yang S, et al. The Arabidopsis SWI2/SNF2 Chromatin Remodeling ATPase BRAHMA Targets Directly to PINs and Is Required for Root Stem Cell Niche Maintenance. Plant Cell, 2015. 27(6): p. 1670-80 [PMID:25991732] Jia Y, et al. The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development. J. Exp. Bot., 2015. 66(15): p. 4631-42 [PMID:25998905] Zhang M, et al. A tetratricopeptide repeat domain-containing protein SSR1 located in mitochondria is involved in root development and auxin polar transport in Arabidopsis. Plant J., 2015. 83(4): p. 582-99 [PMID:26072661] Shinohara H,Mori A,Yasue N,Sumida K,Matsubayashi Y Identification of three LRR-RKs involved in perception of root meristem growth factor in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A., 2016. 113(14): p. 3897-902 [PMID:27001831] Ou Y, et al. RGF1 INSENSITIVE 1 to 5, a group of LRR receptor-like kinases, are essential for the perception of root meristem growth factor 1 in Arabidopsis thaliana. Cell Res., 2016. 26(6): p. 686-98 [PMID:27229312] García-Cruz KV, et al. The MADS-box XAANTAL1 increases proliferation at the Arabidopsis root stem-cell niche and participates in transition to differentiation by regulating cell-cycle components. Ann. Bot., 2018. [PMID:27474508] Santuari L, et al. The PLETHORA Gene Regulatory Network Guides Growth and Cell Differentiation in Arabidopsis Roots. Plant Cell, 2016. 28(12): p. 2937-2951 [PMID:27920338] Franssen HJ,Kulikova O,Willemsen V,Heidstra R Cis-regulatory PLETHORA promoter elements directing root and nodule expression are conserved between Arabidopsis thaliana and Medicago truncatula. Plant Signal Behav, 2017. 12(2): p. e1278102 [PMID:28067580] Promchuea S,Zhu Y,Chen Z,Zhang J,Gong Z ARF2 coordinates with PLETHORAs and PINs to orchestrate ABA-mediated root meristem activity in Arabidopsis . J Integr Plant Biol, 2017. 59(1): p. 30-43 [PMID:28074634] Du Y,Scheres B PLETHORA transcription factors orchestrate de novo organ patterning during Arabidopsis lateral root outgrowth. Proc. Natl. Acad. Sci. U.S.A., 2017. 114(44): p. 11709-11714 [PMID:29078398] Bustillo-Avendaño E, et al. Regulation of Hormonal Control, Cell Reprogramming, and Patterning during De Novo Root Organogenesis. Plant Physiol., 2018. 176(2): p. 1709-1727 [PMID:29233938] Ercoli MF, et al. GIF Transcriptional Coregulators Control Root Meristem Homeostasis. Plant Cell, 2018. 30(2): p. 347-359 [PMID:29352064] Xu C, et al. Control of auxin-induced callus formation by bZIP59-LBD complex in Arabidopsis regeneration. Nat Plants, 2018. 4(2): p. 108-115 [PMID:29358751]