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 NameAIL3, MOE17.15, PLT1
Taxonomic ID
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
AT3G20840.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
          AP2   1 55 
                  s y+GV++++++gr++A+++d  +   g  ++ ++++lg ++ +++Aa+ ++ a++k++g
                  57*******************666664477446**********99*************98 PP

          AP2   3 ykGVrwdkkrgrWvAeIrdpsengkrkrfslgkfgtaeeAakaaiaarkkleg 55 
                  y+GV+++++ grW A+I  +     +k  +lg+f t+eeAa+a++ a+ k++g
                  9***************988532...5************************998 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF008477.2E-11180239IPR001471AP2/ERF domain
CDDcd000188.46E-21180249No hitNo description
SuperFamilySSF541719.15E-16180248IPR016177DNA-binding domain
SMARTSM003802.9E-28181253IPR001471AP2/ERF domain
PROSITE profilePS5103218.716181247IPR001471AP2/ERF domain
Gene3DG3DSA:3.30.730.102.4E-14181247IPR001471AP2/ERF domain
PRINTSPR003675.2E-6182193IPR001471AP2/ERF domain
SuperFamilySSF541719.15E-18282342IPR016177DNA-binding domain
CDDcd000182.40E-24282343No hitNo description
SMARTSM003801.5E-32283347IPR001471AP2/ERF domain
Gene3DG3DSA:3.30.730.104.8E-18283341IPR001471AP2/ERF domain
PROSITE profilePS5103219.506283341IPR001471AP2/ERF domain
PfamPF008471.5E-9284333IPR001471AP2/ERF domain
PRINTSPR003675.2E-6323343IPR001471AP2/ERF domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0000723Biological Processtelomere maintenance
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0007389Biological Processpattern specification process
GO:0009734Biological Processauxin-activated signaling pathway
GO:0009873Biological Processethylene-activated signaling pathway
GO:0010449Biological Processroot meristem growth
GO:0019827Biological Processstem cell population maintenance
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
Sequence ? help Back to Top
Protein Sequence    Length: 574 aa     Download sequence    Send to blast
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Expression -- Microarray ? help Back to Top
Source ID E-value
Expression AtlasAT3G20840-
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL 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}.
UniprotTISSUE 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
TAIREncodes 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.
UniProtProbably 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
  1. 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]
  2. 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]
  3. 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]
  4. The abo8 mutation affects the expression of PLT1 and PLT2; plt1 and plt2 mutants are sensitive to ABA in root growth
    [PMID: 25522358]
  5. 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
Motif logo
Cis-element ? help Back to Top
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By auxin accumulation. {ECO:0000269|PubMed:15454085}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
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 ExpressAT3G20840
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAY5065490.0AY506549.1 Arabidopsis thaliana PLETHORA1 (PLT1) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_188720.20.0Integrase-type DNA-binding superfamily protein
SwissprotQ5YGP80.0PLET1_ARATH; AP2-like ethylene-responsive transcription factor PLT1
TrEMBLD7KZX20.0D7KZX2_ARALL; Uncharacterized protein
STRINGAT3G20840.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Representative plantOGRP11217209
Publications ? help Back to Top
  1. Riechmann JL, et al.
    Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
    Science, 2000. 290(5499): p. 2105-10
  2. Aida M, et al.
    The PLETHORA genes mediate patterning of the Arabidopsis root stem cell niche.
    Cell, 2004. 119(1): p. 109-20
  3. Blilou I, et al.
    The PIN auxin efflux facilitator network controls growth and patterning in Arabidopsis roots.
    Nature, 2005. 433(7021): p. 39-44
  4. 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
  5. 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
  6. 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
  7. 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
  8. Xu J, et al.
    A molecular framework for plant regeneration.
    Science, 2006. 311(5759): p. 385-8
  9. Dello Ioio R, et al.
    Cytokinins determine Arabidopsis root-meristem size by controlling cell differentiation.
    Curr. Biol., 2007. 17(8): p. 678-82
  10. Galinha C, et al.
    PLETHORA proteins as dose-dependent master regulators of Arabidopsis root development.
    Nature, 2007. 449(7165): p. 1053-7
  11. Iyer-Pascuzzi AS,Benfey PN
    Transcriptional networks in root cell fate specification.
    Biochim. Biophys. Acta, 2009. 1789(4): p. 315-25
  12. 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
  13. 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
  14. 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
  15. 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
  16. Smith ZR,Long JA
    Control of Arabidopsis apical-basal embryo polarity by antagonistic transcription factors.
    Nature, 2010. 464(7287): p. 423-6
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. Peng Y, et al.
    Control of root meristem size by DA1-RELATED PROTEIN2 in Arabidopsis.
    Plant Physiol., 2013. 161(3): p. 1542-56
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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
  37. 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
  38. 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
  39. Jia Y, et al.
    The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development.
    J. Exp. Bot., 2015. 66(15): p. 4631-42
  40. 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
  41. 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
  42. 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
  43. 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.
  44. 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
  45. 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
  46. 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
  47. 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
  48. 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
  49. Ercoli MF, et al.
    GIF Transcriptional Coregulators Control Root Meristem Homeostasis.
    Plant Cell, 2018. 30(2): p. 347-359
  50. 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