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

AT3G11260.1

Common Name

F11B9.18, WOX5, WOX5B

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

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
AT3G11260.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Homeobox	64.5	1.5e-20	21	82	1	57
TT--SS--HHHHHHHHHHHHH.SSS--HHHHHHHHHHC....TS-HHHHHHHHHHHHHHHHC CS Homeobox 1 rrkRttftkeqleeLeelFek.nrypsaeereeLAkkl....gLterqVkvWFqNrRakekk 57 ++ R+++t eql++L +lF+ r+p+++++++++++l +++ ++V++WFqN++a+e++ AT3G11260.1 21 KCGRWNPTVEQLKILTDLFRAgLRTPTTDQIQKISTELsfygKIESKNVFYWFQNHKARERQ 82 568***************99************************************97 PP
2	Wus_type_Homeobox	114.2	6.7e-37	21	84	2	65
Wus_type_Homeobox 2 artRWtPtpeQikiLeelyksGlrtPnkeeiqritaeLeeyGkiedkNVfyWFQNrkaRerqkq 65 ++ RW+Pt eQ+kiL++l+++GlrtP++++iq+i++eL+ yGkie+kNVfyWFQN+kaRerqk+ AT3G11260.1 21 KCGRWNPTVEQLKILTDLFRAGLRTPTTDQIQKISTELSFYGKIESKNVFYWFQNHKARERQKR 84 678***********************************************************95 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50071	10.641	18	83	IPR001356	Homeobox domain
SMART	SM00389	6.2E-4	20	87	IPR001356	Homeobox domain
Pfam	PF00046	1.6E-17	22	82	IPR001356	Homeobox domain
SuperFamily	SSF46689	2.44E-11	23	86	IPR009057	Homeodomain-like
Gene3D	G3DSA:1.10.10.60	8.3E-8	24	82	IPR009057	Homeodomain-like
CDD	cd00086	2.13E-4	24	84	No hit	No description

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0009733	Biological Process	response to auxin
GO:0010078	Biological Process	maintenance of root meristem identity
GO:1902459	Biological Process	positive regulation of stem cell population maintenance
GO:0005634	Cellular Component	nucleus
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0005515	Molecular Function	protein binding
GO:0043565	Molecular Function	sequence-specific DNA binding

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0020149	anatomy	quiescent center

Sequence ? help Back to Top
Protein Sequence Length: 182 aa Download sequence Send to blast
MSFSVKGRSL RGNNNGGTGT KCGRWNPTVE QLKILTDLFR AGLRTPTTDQ IQKISTELSF 60 YGKIESKNVF YWFQNHKARE RQKRRKISID FDHHHHQPST RDVFEISEED CQEEEKVIET 120 LQLFPVNSFE DSNSKVDKMR ARGNNQYREY IRETTTTSFS PYSSCGAEME HPPPLDLRLS 180 FL

Expression -- Microarray ? help Back to Top
Source	ID
Expression Atlas	AT3G11260
AtGenExpress	AT3G11260

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL 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}.
Uniprot	TISSUE 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
TAIR	Arabidopsis thaliana WOX5 protein mRNA
UniProt	Transcription 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
Importantly, both WOX5 and WUS maintain stem cells in either a root or shoot context. [PMID: 17429400] 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] Studies indicate that the shoot and root meristems are promoted by WUSCHEL (WUS) and WOX5. [PMID: 22076631] WOX5-IAA17 feedback circuit is essential for the maintenance of auxin gradient in the root tip. [PMID: 23939433] 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] ROW1 is essential for quiescent centre maintenance and for stem cell niche development through the repression of WOX5 in the proximal meristem. [PMID: 25631790] Results show that ACR4 phosphorylates WOX5 through four phosphorylation sites within the WOX5 protein sequence. [PMID: 25756623] 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] WOX5 plays a role in root stem cell niche maintenance. [PMID: 26440429] 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
Source	Link
PlantRegMap	AT3G11260.1

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

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
AHD	auxin

Interaction ? help Back to Top
Source	Intact With
BioGRID	AT3G60630, AT5G26170

Phenotype -- Disruption Phenotype ? help Back to Top
Source	Description
UniProt	DISRUPTION 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 Express	AT3G11260

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AY251398	0.0	AY251398.1 Arabidopsis thaliana WOX5 protein mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_187735.2	1e-136	WUSCHEL related homeobox 5
Swissprot	Q8H1D2	1e-137	WOX5_ARATH; WUSCHEL-related homeobox 5
TrEMBL	A0A384KT15	1e-135	A0A384KT15_ARATH; WOX5B
TrEMBL	C0SVA6	1e-135	C0SVA6_ARATH; Uncharacterized protein At3g11260 (Fragment)
STRING	AT3G11260.1	1e-135	(Arabidopsis thaliana)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM4014	28	57
Representative plant	OGRP8406	11	16

Link Out ? help Back to Top
Phytozome	AT3G11260.1
Entrez Gene	820297
iHOP	AT3G11260
wikigenes	AT3G11260

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] R Rapid identification of Arabidopsis insertion mutants by non-radioactive detection of T-DNA tagged genes. Plant J., 2002. 32(2): p. 243-53 [PMID:12383089] 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 [PMID:14711878] 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 [PMID:16262712] Sarkar AK, et al. Conserved factors regulate signalling in Arabidopsis thaliana shoot and root stem cell organizers. Nature, 2007. 446(7137): p. 811-4 [PMID:17429400] 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 [PMID:18426584] 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 [PMID:18606144] Rebocho AB, et al. Role of EVERGREEN in the development of the cymose petunia inflorescence. Dev. Cell, 2008. 15(3): p. 437-47 [PMID:18804438] 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 [PMID:19387013] 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 [PMID:19398337] 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 [PMID:19639337] 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 [PMID:19820344] 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] 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 [PMID:20729381] 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 [PMID:20920363] 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 [PMID:20977659] 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] 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 [PMID:21460611] 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 [PMID:21744091] 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 [PMID:22076631] 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 [PMID:22232385] Kiyohara S,Sawa S CLE signaling systems during plant development and nematode infection. Plant Cell Physiol., 2012. 53(12): p. 1989-99 [PMID:23045524] 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 [PMID:23062007] 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] 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 [PMID:23939433] 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 [PMID:24043854] 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 [PMID:24056047] 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] 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 [PMID:24635769] 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 [PMID:25127220] 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 [PMID:25256342] Zhou Y, et al. Control of plant stem cell function by conserved interacting transcriptional regulators. Nature, 2015. 517(7534): p. 377-80 [PMID:25363783] 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 [PMID:25438658] 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 [PMID:25631790] 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 [PMID:25642237] 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] 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 [PMID:25756623] 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] 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 [PMID:26019259] 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 [PMID:26028217] 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] 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 [PMID:26440429] 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 [PMID:27784768] 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 [PMID:28053005] 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 [PMID:28195159] 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 [PMID:28426669] Long Y, et al. In vivo FRET-FLIM reveals cell-type-specific protein interactions in Arabidopsis roots. Nature, 2017. 548(7665): p. 97-102 [PMID:28746306] 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 [PMID:28798767] 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 [PMID:28975033] 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. [PMID:29242230] 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] Dolzblasz A, et al. Impairment of Meristem Proliferation in Plants Lacking the Mitochondrial Protease AtFTSH4. Int J Mol Sci, 2018. [PMID:29538317]