PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT3G11260.1
Common NameF11B9.18, WOX5, WOX5B
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 WOX
Protein Properties Length: 182aa    MW: 21225.7 Da    PI: 8.4766
Description WUSCHEL related homeobox 5
Gene Model
Gene Model ID Type Source Coding Sequence
AT3G11260.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
     Homeobox  1 rrkRttftkeqleeLeelFek.nrypsaeereeLAkkl....gLterqVkvWFqNrRakekk 57
                 ++ R+++t eql++L +lF+   r+p+++++++++++l    +++ ++V++WFqN++a+e++
                 568*****************99**************************************97 PP

  Wus_type_Homeobox  2 artRWtPtpeQikiLeelyksGlrtPnkeeiqritaeLeeyGkiedkNVfyWFQNrkaRerqkq 65
                       ++ RW+Pt eQ+kiL++l+++GlrtP++++iq+i++eL+ yGkie+kNVfyWFQN+kaRerqk+
                       678***********************************************************95 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5007110.6411883IPR001356Homeobox domain
SMARTSM003896.2E-42087IPR001356Homeobox domain
PfamPF000461.6E-172282IPR001356Homeobox domain
CDDcd000862.13E-42484No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009733Biological Processresponse to auxin
GO:0010078Biological Processmaintenance of root meristem identity
GO:1902459Biological Processpositive regulation of stem cell population maintenance
GO:0005634Cellular Componentnucleus
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0005515Molecular Functionprotein binding
GO:0043565Molecular Functionsequence-specific DNA binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0020149anatomyquiescent center
Sequence ? help Back to Top
Protein Sequence    Length: 182 aa     Download sequence    Send to blast
Expression -- Microarray ? help Back to Top
Source ID
Expression AtlasAT3G11260
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Specifically expressed in the hypophysis of the majority of early globular embryos, approximately one round of cell division after the 16-cell stage, but never at the 16-cell stage itself. After the division of the hypophysis, it is detected in the upper lens-shaped cell that gives rise to the QC, but not in the lower daughter cell that gives rise to the central root cap. Subsequently, in heart stage and bent cotyledon stage embryos, it is detected in the four cells of the QC, which are the direct descendants of the lens-shaped cell. Also expressed in patches of cells that appeared associated with the vascular primordium of the cotyledons. This expression is strongest in late heart stage embryos and then gradually decreases. {ECO:0000269|PubMed:14711878}.
UniprotTISSUE SPECIFICITY: Specifically expressed in the central cells of a quiescent center (QC) of the root. {ECO:0000269|PubMed:14711878}.
Functional Description ? help Back to Top
Source Description
TAIRArabidopsis thaliana WOX5 protein mRNA
UniProtTranscription factor, which may be involved in the specification and maintenance of the stem cells (QC cells) in the root apical meristem (RAM). {ECO:0000269|PubMed:25631790}.
Function -- GeneRIF ? help Back to Top
  1. Importantly, both WOX5 and WUS maintain stem cells in either a root or shoot context.
    [PMID: 17429400]
  2. The MKO1 gene plays an important role in the maintenance of the root apical meristem proliferative capacity and indeterminate root growth, which apparently acts independently of the SCR/SHR and WOX5 regulatory pathways.
    [PMID: 21744091]
  3. Studies indicate that the shoot and root meristems are promoted by WUSCHEL (WUS) and WOX5.
    [PMID: 22076631]
  4. WOX5-IAA17 feedback circuit is essential for the maintenance of auxin gradient in the root tip.
    [PMID: 23939433]
  5. WOX5 restrains cell division in the cells of the quiescent center, thereby establishing quiescence. In contrast, WOX5 and CYCD3;3/CYCD1;1 both promote cell proliferation in the nascent columella.
    [PMID: 25127220]
  6. ROW1 is essential for quiescent centre maintenance and for stem cell niche development through the repression of WOX5 in the proximal meristem.
    [PMID: 25631790]
  7. Results show that ACR4 phosphorylates WOX5 through four phosphorylation sites within the WOX5 protein sequence.
    [PMID: 25756623]
  8. WOX5 signals from the quiescent centre to promote columella stem cell (CSC) fate, while CLE40 is secreted from the differentiated columella cells to promote differentiation.
    [PMID: 26019259]
  9. WOX5 plays a role in root stem cell niche maintenance.
    [PMID: 26440429]
  10. the expression switch from WOX11/12 to WOX5/7 is critical for initiation of the root primordium during de novo root organogenesis.
    [PMID: 27784768]
Cis-element ? help Back to Top
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 AT2G28350 (R), AT2G33880 (A), AT4G30080 (R), AT5G45980 (A)
Regulation -- Hormone ? help Back to Top
Source Hormone
Interaction ? help Back to Top
Source Intact With
BioGRIDAT3G60630, AT5G26170
Phenotype -- Disruption Phenotype ? help Back to Top
Source Description
UniProtDISRUPTION PHENOTYPE: Abnormal quiescent center (QC) in the root apical meristem (RAM) and defects in cell differentiation. {ECO:0000269|PubMed:25631790}.
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT3G11260
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAY2513980.0AY251398.1 Arabidopsis thaliana WOX5 protein mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_187735.21e-136WUSCHEL related homeobox 5
SwissprotQ8H1D21e-137WOX5_ARATH; WUSCHEL-related homeobox 5
TrEMBLA0A384KT151e-135A0A384KT15_ARATH; WOX5B
TrEMBLC0SVA61e-135C0SVA6_ARATH; Uncharacterized protein At3g11260 (Fragment)
STRINGAT3G11260.11e-135(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Representative plantOGRP84061116
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. R
    Rapid identification of Arabidopsis insertion mutants by non-radioactive detection of T-DNA tagged genes.
    Plant J., 2002. 32(2): p. 243-53
  3. Haecker A, et al.
    Expression dynamics of WOX genes mark cell fate decisions during early embryonic patterning in Arabidopsis thaliana.
    Development, 2004. 131(3): p. 657-68
  4. Gonzali S, et al.
    A turanose-insensitive mutant suggests a role for WOX5 in auxin homeostasis in Arabidopsis thaliana.
    Plant J., 2005. 44(4): p. 633-45
  5. Sarkar AK, et al.
    Conserved factors regulate signalling in Arabidopsis thaliana shoot and root stem cell organizers.
    Nature, 2007. 446(7137): p. 811-4
  6. Conte MG,Gaillard S,Droc G,Perin C
    Phylogenomics of plant genomes: a methodology for genome-wide searches for orthologs in plants.
    BMC Genomics, 2008. 9: p. 183
  7. Song SK,Hofhuis H,Lee MM,Clark SE
    Key divisions in the early Arabidopsis embryo require POL and PLL1 phosphatases to establish the root stem cell organizer and vascular axis.
    Dev. Cell, 2008. 15(1): p. 98-109
  8. Rebocho AB, et al.
    Role of EVERGREEN in the development of the cymose petunia inflorescence.
    Dev. Cell, 2008. 15(3): p. 437-47
  9. Nardmann J,Reisewitz P,Werr W
    Discrete shoot and root stem cell-promoting WUS/WOX5 functions are an evolutionary innovation of angiosperms.
    Mol. Biol. Evol., 2009. 26(8): p. 1745-55
  10. Stahl Y,Wink RH,Ingram GC,Simon R
    A signaling module controlling the stem cell niche in Arabidopsis root meristems.
    Curr. Biol., 2009. 19(11): p. 909-14
  11. Chen SK, et al.
    The association of homeobox gene expression with stem cell formation and morphogenesis in cultured Medicago truncatula.
    Planta, 2009. 230(4): p. 827-40
  12. Stahl Y,Simon R
    Is the Arabidopsis root niche protected by sequestration of the CLE40 signal by its putative receptor ACR4?
    Plant Signal Behav, 2009. 4(7): p. 634-5
  13. 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
  14. Hirakawa Y,Kondo Y,Fukuda H
    TDIF peptide signaling regulates vascular stem cell proliferation via the WOX4 homeobox gene in Arabidopsis.
    Plant Cell, 2010. 22(8): p. 2618-29
  15. Azpeitia E,Ben
    Single-cell and coupled GRN models of cell patterning in the Arabidopsis thaliana root stem cell niche.
    BMC Syst Biol, 2010. 4: p. 134
  16. Zhang X,Zong J,Liu J,Yin J,Zhang D
    Genome-wide analysis of WOX gene family in rice, sorghum, maize, Arabidopsis and poplar.
    J Integr Plant Biol, 2010. 52(11): p. 1016-26
  17. 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
  18. Gagne JM,Gish LA,Clark SE
    The role of the acyl modification, palmitoylation, in Arabidopsis stem cell regulation.
    Plant Signal Behav, 2010. 5(8): p. 1048-51
  19. Hern
    Apical meristem exhaustion during determinate primary root growth in the moots koom 1 mutant of Arabidopsis thaliana.
    Planta, 2011. 234(6): p. 1163-77
  20. Nardmann J,Werr W
    The invention of WUS-like stem cell-promoting functions in plants predates leptosporangiate ferns.
    Plant Mol. Biol., 2012. 78(1-2): p. 123-34
  21. Osipova MA, et al.
    Wuschel-related homeobox5 gene expression and interaction of CLE peptides with components of the systemic control add two pieces to the puzzle of autoregulation of nodulation.
    Plant Physiol., 2012. 158(3): p. 1329-41
  22. Kiyohara S,Sawa S
    CLE signaling systems during plant development and nematode infection.
    Plant Cell Physiol., 2012. 53(12): p. 1989-99
  23. Sang Y, et al.
    Mutations in two non-canonical Arabidopsis SWI2/SNF2 chromatin remodeling ATPases cause embryogenesis and stem cell maintenance defects.
    Plant J., 2012. 72(6): p. 1000-14
  24. 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
  25. Tian H, et al.
    WOX5-IAA17 feedback circuit-mediated cellular auxin response is crucial for the patterning of root stem cell niches in Arabidopsis.
    Mol Plant, 2014. 7(2): p. 277-89
  26. Chu H, et al.
    A CLE-WOX signalling module regulates root meristem maintenance and vascular tissue development in rice.
    J. Exp. Bot., 2013. 64(17): p. 5359-69
  27. Tian H,Niu T,Yu Q,Quan T,Ding Z
    Auxin gradient is crucial for the maintenance of root distal stem cell identity in Arabidopsis.
    Plant Signal Behav, 2013. 8(12): p. e26429
  28. 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
  29. Reyes-Hernández BJ, et al.
    The root indeterminacy-to-determinacy developmental switch is operated through a folate-dependent pathway in Arabidopsis thaliana.
    New Phytol., 2014. 202(4): p. 1223-36
  30. Forzani C, et al.
    WOX5 suppresses CYCLIN D activity to establish quiescence at the center of the root stem cell niche.
    Curr. Biol., 2014. 24(16): p. 1939-44
  31. Bennett T,van den Toorn A,Willemsen V,Scheres B
    Precise control of plant stem cell activity through parallel regulatory inputs.
    Development, 2014. 141(21): p. 4055-64
  32. Zhou Y, et al.
    Control of plant stem cell function by conserved interacting transcriptional regulators.
    Nature, 2015. 517(7534): p. 377-80
  33. Ji H, et al.
    PRL1 modulates root stem cell niche activity and meristem size through WOX5 and PLTs in Arabidopsis.
    Plant J., 2015. 81(3): p. 399-412
  34. Zhang Y,Jiao Y,Liu Z,Zhu YX
    ROW1 maintains quiescent centre identity by confining WOX5 expression to specific cells.
    Nat Commun, 2015. 6: p. 6003
  35. Su YH,Liu YB,Bai B,Zhang XS
    Establishment of embryonic shoot-root axis is involved in auxin and cytokinin response during Arabidopsis somatic embryogenesis.
    Front Plant Sci, 2014. 5: p. 792
  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. Meyer MR,Shah S,Zhang J,Rohrs H,Rao AG
    Evidence for intermolecular interactions between the intracellular domains of the arabidopsis receptor-like kinase ACR4, its homologs and the Wox5 transcription factor.
    PLoS ONE, 2015. 10(3): p. e0118861
  38. Jia Y, et al.
    The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development.
    J. Exp. Bot., 2015. 66(15): p. 4631-42
  39. Richards S,Wink RH,Simon R
    Mathematical modelling of WOX5- and CLE40-mediated columella stem cell homeostasis in Arabidopsis.
    J. Exp. Bot., 2015. 66(17): p. 5375-84
  40. Pi L, et al.
    Organizer-Derived WOX5 Signal Maintains Root Columella Stem Cells through Chromatin-Mediated Repression of CDF4 Expression.
    Dev. Cell, 2015. 33(5): p. 576-88
  41. 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
  42. Kong X,Lu S,Tian H,Ding Z
    WOX5 is Shining in the Root Stem Cell Niche.
    Trends Plant Sci., 2015. 20(10): p. 601-603
  43. Hu X,Xu L
    Transcription Factors WOX11/12 Directly Activate WOX5/7 to Promote Root Primordia Initiation and Organogenesis.
    Plant Physiol., 2016. 172(4): p. 2363-2373
  44. Zhang Y,Jiao Y,Jiao H,Zhao H,Zhu YX
    Two-Step Functional Innovation of the Stem-Cell Factors WUS/WOX5 during Plant Evolution.
    Mol. Biol. Evol., 2017. 34(3): p. 640-653
  45. Singh S, et al.
    Sirtinol, a Sir2 protein inhibitor, affects stem cell maintenance and root development in Arabidopsis thaliana by modulating auxin-cytokinin signaling components.
    Sci Rep, 2017. 7: p. 42450
  46. García-Gómez ML,Azpeitia E,Álvarez-Buylla ER
    A dynamic genetic-hormonal regulatory network model explains multiple cellular behaviors of the root apical meristem of Arabidopsis thaliana.
    PLoS Comput. Biol., 2017. 13(4): p. e1005488
  47. Long Y, et al.
    In vivo FRET-FLIM reveals cell-type-specific protein interactions in Arabidopsis roots.
    Nature, 2017. 548(7665): p. 97-102
  48. Bruno L, et al.
    In Arabidopsis thaliana Cadmium Impact on the Growth of Primary Root by Altering SCR Expression and Auxin-Cytokinin Cross-Talk.
    Front Plant Sci, 2017. 8: p. 1323
  49. Hu B, et al.
    Divergent regeneration-competent cells adopt a common mechanism for callus initiation in angiosperms.
    Regeneration (Oxf), 2017. 4(3): p. 132-139
  50. Lozano-Elena F,Planas-Riverola A,Vilarrasa-Blasi J,Schwab R,Caño-Delgado AI
    Paracrine brassinosteroid signaling at the stem cell niche controls cellular regeneration.
    J. Cell. Sci., 2019.
  51. 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
  52. Dolzblasz A, et al.
    Impairment of Meristem Proliferation in Plants Lacking the Mitochondrial Protease AtFTSH4.
    Int J Mol Sci, 2018.