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

AT5G22220.3

Common Name

ATE2FB, E2F1, E2FB, T6G21

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

E2F/DP

Protein Properties

Length: 466aa MW: 51460.2 Da PI: 4.4025

Description

E2F transcription factor 1

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT5G22220.3	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	E2F_TDP	86.6	1.9e-27	129	194	1	71
E2F_TDP 1 rkeksLrlltqkflkllekseegivtlnevakeLvsedvknkrRRiYDilNVLealnliekkekneirwkg 71 r+++sL+llt+kf++l++++e+gi++ln++a++L +v ++RRiYDi+NVLe+++liek+ kn+i+wkg AT5G22220.3 129 RYDSSLGLLTKKFINLIKQAEDGILDLNKAADTL---EV--QKRRIYDITNVLEGIGLIEKTLKNRIQWKG 194 6899****************************...99..**************************98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:1.10.10.10	3.8E-29	126	196	IPR011991	Winged helix-turn-helix DNA-binding domain
SuperFamily	SSF46785	2.58E-17	129	192	IPR011991	Winged helix-turn-helix DNA-binding domain
SMART	SM01372	5.9E-35	129	194	IPR003316	E2F/DP family, winged-helix DNA-binding domain
Pfam	PF02319	1.6E-24	131	194	IPR003316	E2F/DP family, winged-helix DNA-binding domain
CDD	cd14660	9.16E-46	205	310	No hit	No description
SuperFamily	SSF144074	6.28E-32	207	310	No hit	No description
Pfam	PF16421	3.9E-32	210	308	IPR032198	E2F transcription factor, CC-MB domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0008284	Biological Process	positive regulation of cell proliferation
GO:0009733	Biological Process	response to auxin
GO:0010090	Biological Process	trichome morphogenesis
GO:0045893	Biological Process	positive regulation of transcription, DNA-templated
GO:0051302	Biological Process	regulation of cell division
GO:0051446	Biological Process	positive regulation of meiotic cell cycle
GO:0005634	Cellular Component	nucleus
GO:0005667	Cellular Component	transcription factor complex
GO:0005737	Cellular Component	cytoplasm
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:0000013	anatomy	cauline leaf
PO:0000016	anatomy	lateral root primordium
PO:0000017	anatomy	vascular leaf primordium
PO:0000035	anatomy	cotyledon vascular system
PO:0000037	anatomy	shoot apex
PO:0000084	anatomy	plant sperm cell
PO:0000230	anatomy	inflorescence meristem
PO:0000232	anatomy	axillary bud meristem
PO:0000293	anatomy	guard cell
PO:0006504	anatomy	leaf trichome
PO:0008019	anatomy	leaf lamina base
PO:0009005	anatomy	root
PO:0009006	anatomy	shoot system
PO:0009009	anatomy	plant embryo
PO:0009010	anatomy	seed
PO:0009025	anatomy	vascular leaf
PO:0009029	anatomy	stamen
PO:0009030	anatomy	carpel
PO:0009031	anatomy	sepal
PO:0009032	anatomy	petal
PO:0009046	anatomy	flower
PO:0009047	anatomy	stem
PO:0009052	anatomy	flower pedicel
PO:0009062	anatomy	gynoecium
PO:0009066	anatomy	anther
PO:0009072	anatomy	plant ovary
PO:0009073	anatomy	stigma
PO:0009074	anatomy	style
PO:0020030	anatomy	cotyledon
PO:0020038	anatomy	petiole
PO:0020100	anatomy	hypocotyl
PO:0020137	anatomy	leaf apex
PO:0020148	anatomy	shoot apical meristem
PO:0025022	anatomy	collective leaf structure
PO:0025257	anatomy	primary root elongation zone
PO:0025281	anatomy	pollen
PO:0001054	developmental stage	vascular leaf senescent stage
PO:0001078	developmental stage	plant embryo cotyledonary stage
PO:0001081	developmental stage	mature plant embryo stage
PO:0001185	developmental stage	plant embryo globular stage
PO:0004507	developmental stage	plant embryo bilateral stage
PO:0007095	developmental stage	LP.08 eight leaves visible stage
PO:0007103	developmental stage	LP.10 ten leaves visible stage
PO:0007115	developmental stage	LP.04 four leaves visible stage
PO:0007123	developmental stage	LP.06 six leaves visible stage
PO:0007131	developmental stage	seedling development stage
PO:0007611	developmental stage	petal differentiation and expansion stage
PO:0007616	developmental stage	flowering stage

Sequence ? help Back to Top
Protein Sequence Length: 466 aa Download sequence Send to blast
MSEEVPQQFP SSKRQLHPSL SSMKPPLVAP GEYHRFDAAE TRGGGAVADQ VVSDAIVIKS 60 TLKRKTDLVN QIVEVNELNT GVLQTPVSGK GGKAKKTSRS AKSNKSGTLA SGSNAGSPGN 120 NFAQAGTCRY DSSLGLLTKK FINLIKQAED GILDLNKAAD TLEVQKRRIY DITNVLEGIG 180 LIEKTLKNRI QWKGLDVSKP GETIESIANL QDEVQNLAAE EARLDDQIRE SQERLTSLSE 240 DENNKRLLFV TENDIKNLPC FQNKTLIAVK APHGTTLEVP DPDEAGGYQR RYRIILRSTM 300 GPIDVYLVSQ FEESFEDIPQ ADEPSNVPDE PSNVPDVPSN LPSTSGLPEN HDVSMPMKEE 360 STERNMETQE VDDTQRVYSD IESHDFVDGI MKIVPPDLDM GVDYWFRSEV GEVSITDMWP 420 DEYWNQMITF DQDHAGPSDN KILEQPQTPS SPTPEESTAT RSPTGS

Sequence ? help Back to Top

Protein Sequence Length: 466 aa Download sequence Send to blast

MSEEVPQQFP SSKRQLHPSL SSMKPPLVAP GEYHRFDAAE TRGGGAVADQ VVSDAIVIKS  60
TLKRKTDLVN QIVEVNELNT GVLQTPVSGK GGKAKKTSRS AKSNKSGTLA SGSNAGSPGN  120
NFAQAGTCRY DSSLGLLTKK FINLIKQAED GILDLNKAAD TLEVQKRRIY DITNVLEGIG  180
LIEKTLKNRI QWKGLDVSKP GETIESIANL QDEVQNLAAE EARLDDQIRE SQERLTSLSE  240
DENNKRLLFV TENDIKNLPC FQNKTLIAVK APHGTTLEVP DPDEAGGYQR RYRIILRSTM  300
GPIDVYLVSQ FEESFEDIPQ ADEPSNVPDE PSNVPDVPSN LPSTSGLPEN HDVSMPMKEE  360
STERNMETQE VDDTQRVYSD IESHDFVDGI MKIVPPDLDM GVDYWFRSEV GEVSITDMWP  420
DEYWNQMITF DQDHAGPSDN KILEQPQTPS SPTPEESTAT RSPTGS

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1cf7_A	1e-24	129	195	7	74	PROTEIN (TRANSCRIPTION FACTOR E2F-4)
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
At.10189	0.0	flower

Expression -- Microarray ? help Back to Top
Source	ID	E-value
Genevisible	245685_at	0.0
Expression Atlas	AT5G22220	-
AtGenExpress	AT5G22220	-
ATTED-II	AT5G22220	-

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Expressed in a cell cycle-dependent manner. Most abundant at the G1/S transition. Lower but constant level in the following phases. {ECO:0000269\|PubMed:11669580, ECO:0000269\|PubMed:11786543, ECO:0000269\|PubMed:16514015}.
Uniprot	TISSUE SPECIFICITY: Expressed in proliferating cells and several differentiated tissues. Detected in inflorescence and shoot apical meristems, cotyledonary vascular tissues, leaf primordia, young leaves, base of trichomes, central cylinder and elongation zone of roots, lateral root primordia, flowers, pistils of immature flowers and pollen grains. {ECO:0000269\|PubMed:16514015}.

Functional Description ? help Back to Top
Source	Description
TAIR	Member of the E2F transcription factors, (cell cycle genes), key components of the cyclin D/retinoblastoma/E2F pathway. Binds DPA and RBR1 proteins. Expressed throughout the cell cycle. Abundance increased by auxin through stabilization of the protein. Elevates CDK levels and activity, even under hormone-free conditions. Promotes cell division and shortens cell doubling time, inhibits cell growth. Transgenic plants overexpressing AtE2Fa contained an increased level of AtE2Fb transcripts that is paralleled by an increase in the amount of the AtE2Fb protein, suggesting that AtE2Fb expression might actually be up-regulated by the AtE2Fa transcription factor.
UniProt	Transcription activator that binds DNA cooperatively with DP proteins through the E2 recognition site, 5'-TTTC[CG]CGC-3' found in the promoter region of a number of genes whose products are involved in cell cycle regulation or in DNA replication. The binding of retinoblastoma-related proteins represses transactivation. Involved in the control of cell-cycle progression from G1 to S phase and from G2 to M phase. Stimulates cell proliferation and delays differentiation. Represses cell enlargement and endoreduplication in auxin-free conditions. {ECO:0000269\|PubMed:11669580, ECO:0000269\|PubMed:11786543, ECO:0000269\|PubMed:11862494, ECO:0000269\|PubMed:11891240, ECO:0000269\|PubMed:12913157, ECO:0000269\|PubMed:16055635, ECO:0000269\|PubMed:16514015}.

Function -- GeneRIF ? help Back to Top
Results suggest that E2FB is one of the key targets for auxin to determine whether cells proliferate or whether they exit the cell cycle, enlarge, and endoreduplicate their DNA. [PMID: 16055635] AtE2Fa and AtE2Fb have specific expression patterns and may play similar but distinct roles during cell cycle progression. [PMID: 16514015] The authors found that S6K1 associates with the Retinoblastoma-related 1 (RBR1)-E2FB complex and this is partly mediated by its N-terminal LVxCxE motif. [PMID: 20683442] The Arabidopsis (Arabidopsis thaliana) DEL1 gene was identified as a transcriptional target of the classical E2Fb and E2Fc transcription factors. [PMID: 21908689] S6K1 interacts with retinoblastoma protein RBR via its N-terminal RBR binding motif, promotes its nuclear localization and consequent RBR-dependent repression of cell cycle genes through transcription factor E2FB. [PMID: 23531690] SIM and SMR1 are involved in hyperphosphorylation of the cell-cycle regulator RBR1 and overexpression of E2F target genes. [PMID: 25455564]

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00661	PBM	Transfer from Pp3c1_6880	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT5G22220.3

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Up-regulated by light and by auxin. May be up-regulated by E2FA. {ECO:0000269\|PubMed:16055635, ECO:0000269\|PubMed:16514015, ECO:0000269\|PubMed:18424613}.

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	AT2G36010 (A), AT5G14960 (A)

Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source	Target Gene (A: Activate/R: Repress)
ATRM	AT2G40550(A), AT3G54180(A), AT5G24330(A)

Regulation -- Hormone ? help Back to Top
Source	Hormone
AHD	auxin

Interaction ? help Back to Top
Source	Intact With
IntAct	Search Q9FV71

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT5G22220

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AF242580	0.0	AF242580.1 Arabidopsis thaliana E2F transcription factor-1 E2F1 mRNA, complete cds.
GenBank	AY136479	0.0	AY136479.1 Arabidopsis thaliana expressed protein (At5g22220) mRNA, complete cds.
GenBank	BT006610	0.0	BT006610.1 Arabidopsis thaliana At5g22220 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_001031921.3	0.0	E2F transcription factor 1
Swissprot	Q9FV71	0.0	E2FB_ARATH; Transcription factor E2FB
TrEMBL	A0A178ULG8	0.0	A0A178ULG8_ARATH; E2FB
STRING	AT5G22220.2	0.0	(Arabidopsis thaliana)

Link Out ? help Back to Top
Phytozome	AT5G22220.3
Entrez Gene	832283
iHOP	AT5G22220
wikigenes	AT5G22220

Publications ? help Back to Top
Magyar Z,Atanassova A,De Veylder L,Rombauts S,Inzé D Characterization of two distinct DP-related genes from Arabidopsis thaliana. FEBS Lett., 2000. 486(1): p. 79-87 [PMID:11108847] Riechmann JL, et al. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science, 2000. 290(5499): p. 2105-10 [PMID:11118137] de Jager SM,Menges M,Bauer UM,Murra JA Arabidopsis E2F1 binds a sequence present in the promoter of S-phase-regulated gene AtCDC6 and is a member of a multigene family with differential activities. Plant Mol. Biol., 2001. 47(4): p. 555-68 [PMID:11669580] Mariconti L, et al. The E2F family of transcription factors from Arabidopsis thaliana. Novel and conserved components of the retinoblastoma/E2F pathway in plants. J. Biol. Chem., 2002. 277(12): p. 9911-9 [PMID:11786543] Rossignol P, et al. AtE2F-a and AtDP-a, members of the E2F family of transcription factors, induce Arabidopsis leaf cells to re-enter S phase. Mol. Genet. Genomics, 2002. 266(6): p. 995-1003 [PMID:11862494] Kosugi S,Ohashi Y Interaction of the Arabidopsis E2F and DP proteins confers their concomitant nuclear translocation and transactivation. Plant Physiol., 2002. 128(3): p. 833-43 [PMID:11891240] Vandepoele K, et al. Genome-wide analysis of core cell cycle genes in Arabidopsis. Plant Cell, 2002. 14(4): p. 903-16 [PMID:11971144] Egelkrout EM, et al. Two E2F elements regulate the proliferating cell nuclear antigen promoter differently during leaf development. Plant Cell, 2002. 14(12): p. 3225-36 [PMID:12468739] Kosugi S,Ohashi Y Constitutive E2F expression in tobacco plants exhibits altered cell cycle control and morphological change in a cell type-specific manner. Plant Physiol., 2003. 132(4): p. 2012-22 [PMID:12913157] Yamada K, et al. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science, 2003. 302(5646): p. 842-6 [PMID:14593172] Maiti B, et al. Cloning and characterization of mouse E2F8, a novel mammalian E2F family member capable of blocking cellular proliferation. J. Biol. Chem., 2005. 280(18): p. 18211-20 [PMID:15722552] Magyar Z, et al. The role of the Arabidopsis E2FB transcription factor in regulating auxin-dependent cell division. Plant Cell, 2005. 17(9): p. 2527-41 [PMID:16055635] Sozzani R, et al. Interplay between Arabidopsis activating factors E2Fb and E2Fa in cell cycle progression and development. Plant Physiol., 2006. 140(4): p. 1355-66 [PMID:16514015] Raynaud C, et al. Two cell-cycle regulated SET-domain proteins interact with proliferating cell nuclear antigen (PCNA) in Arabidopsis. Plant J., 2006. 47(3): p. 395-407 [PMID:16771839] L Distinct light-initiated gene expression and cell cycle programs in the shoot apex and cotyledons of Arabidopsis. Plant Cell, 2008. 20(4): p. 947-68 [PMID:18424613] Takahashi N, et al. The DNA replication checkpoint aids survival of plants deficient in the novel replisome factor ETG1. EMBO J., 2008. 27(13): p. 1840-51 [PMID:18528439] Ascencio-Ib Global analysis of Arabidopsis gene expression uncovers a complex array of changes impacting pathogen response and cell cycle during geminivirus infection. Plant Physiol., 2008. 148(1): p. 436-54 [PMID:18650403] Sozzani R, et al. The E2FD/DEL2 factor is a component of a regulatory network controlling cell proliferation and development in Arabidopsis. Plant Mol. Biol., 2010. 72(4-5): p. 381-95 [PMID:19937368] Boruc J, et al. Functional modules in the Arabidopsis core cell cycle binary protein-protein interaction network. Plant Cell, 2010. 22(4): p. 1264-80 [PMID:20407024] Henriques R, et al. Arabidopsis S6 kinase mutants display chromosome instability and altered RBR1-E2F pathway activity. EMBO J., 2010. 29(17): p. 2979-93 [PMID:20683442] Van Leene J, et al. Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana. Mol. Syst. Biol., 2010. 6: p. 397 [PMID:20706207] Heckmann S, et al. The E2F transcription factor family regulates CENH3 expression in Arabidopsis thaliana. Plant J., 2011. 68(4): p. 646-56 [PMID:21771121] Berckmans B, et al. Light-dependent regulation of DEL1 is determined by the antagonistic action of E2Fb and E2Fc. Plant Physiol., 2011. 157(3): p. 1440-51 [PMID:21908689] Hirano H,Shinmyo A,Sekine M Both negative and positive G1 cell cycle regulators undergo proteasome-dependent degradation during sucrose starvation in Arabidopsis. Plant Signal Behav, 2011. 6(9): p. 1394-6 [PMID:22019639] Heyndrickx KS,Vandepoele K Systematic identification of functional plant modules through the integration of complementary data sources. Plant Physiol., 2012. 159(3): p. 884-901 [PMID:22589469] Henriques R,Magyar Z,B S6K1 and E2FB are in mutually antagonistic regulatory links controlling cell growth and proliferation in Arabidopsis. Plant Signal Behav, 2013. 8(6): p. e24367 [PMID:23531690] Wu M,Liu L,Hijazi H,Chan C A multi-layer inference approach to reconstruct condition-specific genes and their regulation. Bioinformatics, 2013. 29(12): p. 1541-52 [PMID:23610368] Derkacheva M, et al. Arabidopsis MSI1 connects LHP1 to PRC2 complexes. EMBO J., 2013. 32(14): p. 2073-85 [PMID:23778966] Wang S, et al. A noncanonical role for the CKI-RB-E2F cell-cycle signaling pathway in plant effector-triggered immunity. Cell Host Microbe, 2014. 16(6): p. 787-94 [PMID:25455564] 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] Kobayashi K, et al. Transcriptional repression by MYB3R proteins regulates plant organ growth. EMBO J., 2015. 34(15): p. 1992-2007 [PMID:26069325]