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

AT1G51190.1

Common Name

AIL4, F11M15.6, PLT2

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: 568aa MW: 62233.1 Da PI: 6.8282

Description

AP2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT1G51190.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	AP2	47.9	3.4e-15	189	248	1	55
AP2 1 sgykGVrwdkkrgrWvAeIrd.pse.ng..kr.krfslgkfgtaeeAakaaiaarkkleg 55 s y+GV++++++gr++A+++d + g ++ ++++lg ++ +e+Aa+a++ a++k++g AT1G51190.1 189 SIYRGVTRHRWTGRYEAHLWDnSCRrEGqsRKgRQVYLGGYDKEEKAARAYDLAALKYWG 248 57*****************666664477446***********************98 PP
2	AP2	47	6.3e-15	293	342	3	55
AP2 3 ykGVrwdkkrgrWvAeIrdpsengkrkrfslgkfgtaeeAakaaiaarkkleg 55 y+GV+++++ grW A+I + +k +lg+f t+eeAa+a++ a+ k++g AT1G51190.1 293 YRGVTRHHQHGRWQARIGRVAG---NKDLYLGTFSTEEEAAEAYDIAAIKFRG 342 9*************988532...5**********************998 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
CDD	cd00018	2.89E-22	189	258	No hit	No description
SuperFamily	SSF54171	2.94E-17	189	257	IPR016177	DNA-binding domain
Pfam	PF00847	3.3E-12	189	248	IPR001471	AP2/ERF domain
PROSITE profile	PS51032	19.322	190	256	IPR001471	AP2/ERF domain
SMART	SM00380	6.2E-30	190	262	IPR001471	AP2/ERF domain
Gene3D	G3DSA:3.30.730.10	5.5E-16	190	256	IPR001471	AP2/ERF domain
PRINTS	PR00367	5.1E-6	191	202	IPR001471	AP2/ERF domain
SuperFamily	SSF54171	9.15E-18	291	351	IPR016177	DNA-binding domain
CDD	cd00018	3.85E-24	291	352	No hit	No description
PROSITE profile	PS51032	19.506	292	350	IPR001471	AP2/ERF domain
SMART	SM00380	1.5E-32	292	356	IPR001471	AP2/ERF domain
Gene3D	G3DSA:3.30.730.10	4.7E-18	292	350	IPR001471	AP2/ERF domain
Pfam	PF00847	1.5E-9	293	342	IPR001471	AP2/ERF domain
PRINTS	PR00367	5.1E-6	332	352	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:0010073	Biological Process	meristem maintenance
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
GO:0005515	Molecular Function	protein binding

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0009005	anatomy	root
PO:0009029	anatomy	stamen
PO:0009031	anatomy	sepal
PO:0009032	anatomy	petal
PO:0020030	anatomy	cotyledon
PO:0020100	anatomy	hypocotyl

Sequence ? help Back to Top
Protein Sequence Length: 568 aa Download sequence Send to blast
MNSNNWLAFP LSPTHSSLPP HIHSSQNSHF NLGLVNDNID NPFQNQGWNM INPHGGGGEG 60 GEVPKVADFL GVSKSGDHHT DHNLVPYNDI HQTNASDYYF QTNSLLPTVV TCASNAPNNY 120 ELQESAHNLQ SLTLSMGSTG AAAAEVATVK ASPAETSADN SSSTTNTSGG AIVEATPRRT 180 LETFGQRTSI YRGVTRHRWT GRYEAHLWDN SCRREGQSRK GRQVYLGGYD KEEKAARAYD 240 LAALKYWGPS TTTNFPITNY EKEVEEMKNM TRQEFVASIR RKSSGFSRGA SMYRGVTRHH 300 QHGRWQARIG RVAGNKDLYL GTFSTEEEAA EAYDIAAIKF RGLNAVTNFE INRYDVKAIL 360 ESNTLPIGGG AAKRLKEAQA LESSRKREEM IALGSNFHQY GAASGSSSVA SSSRLQLQPY 420 PLSIQQPFEH LHHHQPLLTL QNNNDISQYH DSFSYIQTQL HLHQQQTNNY LQSSSHTSQL 480 YNAYLQSNPG LLHGFVSDNN NTSGFLGNNG IGIGSSSTVG SSAEEEFPAV KVDYDMPPSG 540 GATGYGGWNS GESAQGSNPG GVFTMWNE

Sequence ? help Back to Top

Protein Sequence Length: 568 aa Download sequence Send to blast

MNSNNWLAFP LSPTHSSLPP HIHSSQNSHF NLGLVNDNID NPFQNQGWNM INPHGGGGEG  60
GEVPKVADFL GVSKSGDHHT DHNLVPYNDI HQTNASDYYF QTNSLLPTVV TCASNAPNNY  120
ELQESAHNLQ SLTLSMGSTG AAAAEVATVK ASPAETSADN SSSTTNTSGG AIVEATPRRT  180
LETFGQRTSI YRGVTRHRWT GRYEAHLWDN SCRREGQSRK GRQVYLGGYD KEEKAARAYD  240
LAALKYWGPS TTTNFPITNY EKEVEEMKNM TRQEFVASIR RKSSGFSRGA SMYRGVTRHH  300
QHGRWQARIG RVAGNKDLYL GTFSTEEEAA EAYDIAAIKF RGLNAVTNFE INRYDVKAIL  360
ESNTLPIGGG AAKRLKEAQA LESSRKREEM IALGSNFHQY GAASGSSSVA SSSRLQLQPY  420
PLSIQQPFEH LHHHQPLLTL QNNNDISQYH DSFSYIQTQL HLHQQQTNNY LQSSSHTSQL  480
YNAYLQSNPG LLHGFVSDNN NTSGFLGNNG IGIGSSSTVG SSAEEEFPAV KVDYDMPPSG  540
GATGYGGWNS GESAQGSNPG GVFTMWNE

Expression -- Microarray ? help Back to Top
Source	ID	E-value
GEO	145336608	0.0
Genevisible	265145_at	0.0
Expression Atlas	AT1G51190	-
AtGenExpress	AT1G51190	-
ATTED-II	AT1G51190	-

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]

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT1G51190.1

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	-

Interaction ? help Back to Top
Source	Intact With
IntAct	Search Q5YGP7

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT1G51190

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AY506550	0.0	AY506550.1 Arabidopsis thaliana PLETHORA2 (PLT2) mRNA, complete cds.
GenBank	BT020277	0.0	BT020277.1 Arabidopsis thaliana At1g51190 mRNA, complete cds.
GenBank	BT020460	0.0	BT020460.1 Arabidopsis thaliana At1g51190 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_175530.2	0.0	Integrase-type DNA-binding superfamily protein
Swissprot	Q5YGP7	0.0	PLET2_ARATH; AP2-like ethylene-responsive transcription factor PLT2
TrEMBL	A0A178WB26	0.0	A0A178WB26_ARATH; PLT2
STRING	AT1G51190.1	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	AT1G51190.1
Entrez Gene	841542
iHOP	AT1G51190
wikigenes	AT1G51190

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] 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] 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] Kornet N,Scheres B Members of the GCN5 histone acetyltransferase complex regulate PLETHORA-mediated root stem cell niche maintenance and transit amplifying cell proliferation in Arabidopsis. Plant Cell, 2009. 21(4): p. 1070-9 [PMID:19376933] 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] 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] El Ouakfaoui S, et al. Control of somatic embryogenesis and embryo development by AP2 transcription factors. Plant Mol. Biol., 2010. 74(4-5): p. 313-26 [PMID:20798978] 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] Brady SM, et al. A stele-enriched gene regulatory network in the Arabidopsis root. Mol. Syst. Biol., 2011. 7: p. 459 [PMID:21245844] 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] 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] 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] Kong Y, et al. Tissue-specific expression of SMALL AUXIN UP RNA41 differentially regulates cell expansion and root meristem patterning in Arabidopsis. Plant Cell Physiol., 2013. 54(4): p. 609-21 [PMID:23396598] 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] 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] 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] 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] 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]