PlantTFDB
Plant Transcription Factor Database
v4.0
Previous version: v1.0, v2.0, v3.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT1G28300.1
Common NameF3H9.5, LEC2
Organism
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 B3
Protein Properties Length: 363aa    MW: 41708.4 Da    PI: 5.0397
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
AT1G28300.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B360.33.4e-19172266294
                  EEE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEE.TTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EE CS
           B3   2 fkvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltled.esgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvv 94 
                  +k+l++sdv+++gr+vlpk+ ae++  +++ +e++ ++++d  s +sW++k+++  ++ks++yvl+ ++ eFvk+ng + gDf++++  ++++++l++
  AT1G28300.1 172 EKELKNSDVGSLGRIVLPKRDAEANlpKLSDKEGIVVQMRDvFSMQSWSFKYKFwsNNKSRMYVLE-NTGEFVKQNGAEIGDFLTIY--EDESKNLYF 266
                  799************************77778999******8888*******99888888889999.********************..556766665 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.107.7E-24167276IPR015300DNA-binding pseudobarrel domain
CDDcd100173.47E-22170265No hitNo description
SuperFamilySSF1019361.04E-18171267IPR015300DNA-binding pseudobarrel domain
PROSITE profilePS508639.22171272IPR003340B3 DNA binding domain
SMARTSM010199.1E-20171272IPR003340B3 DNA binding domain
PfamPF023626.2E-16172266IPR003340B3 DNA binding domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0010262Biological Processsomatic embryogenesis
GO:0010344Biological Processseed oilbody biogenesis
GO:0010431Biological Processseed maturation
GO:0010601Biological Processpositive regulation of auxin biosynthetic process
GO:0045893Biological Processpositive regulation of transcription, DNA-templated
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
PO:0000011anatomycultured somatic plant embryo
PO:0001078developmental stageplant embryo cotyledonary stage
PO:0001185developmental stageplant embryo globular stage
PO:0004507developmental stageplant embryo bilateral stage
PO:0007131developmental stageseedling development stage
Sequence ? help Back to Top
Protein Sequence    Length: 363 aa     Download sequence    Send to blast
MDNFLPFPSS NANSVQELSM DPNNNRSHFT TVPTYDHHQA QPHHFLPPFS YPVEQMAAVM  60
NPQPVYLSEC YPQIPVTQTG SEFGSLVGNP CLWQERGGFL DPRMTKMARI NRKNAMMRSR  120
NNSSPNSSPS ELVDSKRQLM MLNLKNNVQI SDKKDSYQQS TFDNKKLRVL CEKELKNSDV  180
GSLGRIVLPK RDAEANLPKL SDKEGIVVQM RDVFSMQSWS FKYKFWSNNK SRMYVLENTG  240
EFVKQNGAEI GDFLTIYEDE SKNLYFAMNG NSGKQNEGRE NESRERNHYE EAMLDYIPRD  300
EEEASIAMLI GNLNDHYPIP NDLMDLTTDL QHHQATSSSM PPEDHAYVGS SDDQVSFNDF  360
EWW
Expression -- Microarray ? help Back to Top
Source ID E-value
Genevisible245669_at0.0
Expression AtlasAT1G28300-
AtGenExpressAT1G28300-
ATTED-IIAT1G28300-
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Expressed during embryo development. {ECO:0000269|PubMed:11573014}.
Functional Description ? help Back to Top
Source Description
TAIRTranscription factor that contains a B3 domain, a DNA-binding motif unique to plants and characteristic of several transcription factors. Plays critical roles both early and late during embryo development. LEC2 RNA accumulates primarily during seed development. LEC2 is required for the maintenance of suspensor morphology, specification of cotyledon identity, progression through the maturation phase, and suppression of premature germination. It establishes a cellular environment sufficient to initiate embryo development - ectopic, postembryonic expression of LEC2 in transgenic plants induces the formation of somatic embryos and other organ-like structures and often confers embryonic characteristics to seedlings and to reproductive and vegetative organs of mature plants.
UniProtTranscription regulator that plays a central role in embryo development. Required for the maintenance of suspensor morphology, specification of cotyledon identity, progression through the maturation phase and suppression of premature germination. Ectopic expression is sufficient to promote somatic embryogenesis. {ECO:0000269|PubMed:11573014, ECO:0000269|PubMed:16492731, ECO:0000269|PubMed:18287041}.
Function -- GeneRIF ? help Back to Top
  1. In this study, it was shown that gibberellin (GA) hormone biosynthesis is regulated by LEC2 and FUS3 pathways.
    [PMID: 15516508]
  2. Loss of embryogenic potential in the lec2 mutant in vitro is not related to the distribution of exogenously applied auxin.
    [PMID: 16034595]
  3. Data show that the induction of LEAFY COTYLEDON 2 leads to the accumulation of storage oil and seed specific mRNAs in leaves, and increases the expression of the seed regulators namely, LEC1, FUS3, and ABI3.
    [PMID: 16107256]
  4. demonstrate that LEC2 directly controls a transcriptional program involved in the maturation phase of seed development
    [PMID: 16492731]
  5. WRINKLED 1 is a target of LEAFY COTYLEDON2 and is necessary for the regulatory action on fatty acid metabolism.
    [PMID: 17419836]
  6. LEC2 causes rapid changes in auxin responses and induces cellular differentiation characteristic of the maturation phase.
    [PMID: 18287041]
  7. revealed differential expression of LEC2 transcripts within a 30 days time course of somatic embryo development.
    [PMID: 19763577]
  8. The central promoter region of OLEOSIN, responsible for seed specificity and LEC2 activation, was determined by 5'-deletion analysis.
    [PMID: 19802745]
  9. LEC2 alters: (1) the delivery of photosynthates from the seed coat to the embryo, (2) carbon partitioning towards different storage compounds, (3) the rate of starch synthesis, and (4) degradation in developing seeds and germination capacity of dry seeds.
    [PMID: 21665323]
  10. Transcriptional regulation of Arabidopsis LEAFY COTYLEDON2 involves a cis-element that regulates trimethylation of histone H3 at lysine-27.
    [PMID: 22080598]
  11. Role and expression pattern of LEC2 in seed development
    [PMID: 22228409]
  12. The analysis indicated that YUCCAs and TAA1, working in the IPA-YUC auxin biosynthesis pathway, are associated with SE induction, and that the expression of three YUCCA genes (YUC1, YUC4 and YUC10) is associated with LEC2 activity.
    [PMID: 23722561]
  13. LEC2 overexpression modifies the morphology and anatomy of leaves by promoting differentiation toward an embryonic pathway.
    [PMID: 23780897]
  14. This study examined the role of ABSCISIC ACID INSENSITIVE3 (ABI3), FUSCA3 (FUS3) and LEAFY COTYLEDON2 (LEC2), in the production of seed reserves in Arabidopsis.
    [PMID: 25840088]
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00032PBM25215497Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT1G28300.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Regulation -- ATRM (Manually Curated Upstream Regulators) ? help Back to Top
Source Upstream Regulator (A: Activate/R: Repress)
ATRM AT1G21970 (A), AT1G54060 (R)
Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source Target Gene (A: Activate/R: Repress)
ATRM AT1G04250(A), AT1G80340(R), AT2G22810(A), AT2G36270(R), AT3G24650(A), AT3G26790(A), AT3G54320(A), AT3G62100(A), AT4G13260(A), AT4G14560(A), AT4G27160(A), AT5G11320(A), AT5G13790(A), AT5G65165(A)
Regulation -- Hormone ? help Back to Top
Source Hormone
AHDabscisic acid
Phenotype -- Disruption Phenotype ? help Back to Top
Source Description
UniProtDISRUPTION PHENOTYPE: Pigmented seeds. Distorted seedlings with elongated hypocotyl and curled cotyledons. Presence of trichomes and accumulation of anthocyanins on cotyledons. Unusual pattern of storage product accumulation in seedlings. {ECO:0000269|PubMed:12244265}.
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT1G28300
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankDQ4462960.0DQ446296.1 Arabidopsis thaliana clone pENTR221-At1g28300 transcriptional factor B3 family protein/leafy cotyledon 2 (At1g28300) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_564304.10.0B3 domain-containing transcription factor LEC2
SwissprotQ1PFR70.0LEC2_ARATH; B3 domain-containing transcription factor LEC2
TrEMBLD7KCU90.0D7KCU9_ARALL; Leafy cotyledon 2
STRINGAT1G28300.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM92622336
Representative plantOGRP7881766
Publications ? help Back to Top
  1. Wehmeyer N,Vierling E
    The expression of small heat shock proteins in seeds responds to discrete developmental signals and suggests a general protective role in desiccation tolerance.
    Plant Physiol., 2000. 122(4): p. 1099-108
    [PMID:10759505]
  2. Riechmann JL, et al.
    Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
    Science, 2000. 290(5499): p. 2105-10
    [PMID:11118137]
  3. Stone SL, et al.
    LEAFY COTYLEDON2 encodes a B3 domain transcription factor that induces embryo development.
    Proc. Natl. Acad. Sci. U.S.A., 2001. 98(20): p. 11806-11
    [PMID:11573014]
  4. Meinke DW,Franzmann LH,Nickle TC,Yeung EC
    Leafy Cotyledon Mutants of Arabidopsis.
    Plant Cell, 1994. 6(8): p. 1049-1064
    [PMID:12244265]
  5. Dean Rider S, et al.
    Coordinate repression of regulators of embryonic identity by PICKLE during germination in Arabidopsis.
    Plant J., 2003. 35(1): p. 33-43
    [PMID:12834400]
  6. Kroj T,Savino G,Valon C,Giraudat J,Parcy F
    Regulation of storage protein gene expression in Arabidopsis.
    Development, 2003. 130(24): p. 6065-73
    [PMID:14597573]
  7. Gong W, et al.
    Genome-wide ORFeome cloning and analysis of Arabidopsis transcription factor genes.
    Plant Physiol., 2004. 135(2): p. 773-82
    [PMID:15208423]
  8. Curaba J, et al.
    AtGA3ox2, a key gene responsible for bioactive gibberellin biosynthesis, is regulated during embryogenesis by LEAFY COTYLEDON2 and FUSCA3 in Arabidopsis.
    Plant Physiol., 2004. 136(3): p. 3660-9
    [PMID:15516508]
  9. Kagaya Y, et al.
    Indirect ABA-dependent regulation of seed storage protein genes by FUSCA3 transcription factor in Arabidopsis.
    Plant Cell Physiol., 2005. 46(2): p. 300-11
    [PMID:15695463]
  10. Tsukagoshi H,Saijo T,Shibata D,Morikami A,Nakamura K
    Analysis of a sugar response mutant of Arabidopsis identified a novel B3 domain protein that functions as an active transcriptional repressor.
    Plant Physiol., 2005. 138(2): p. 675-85
    [PMID:15894743]
  11. Gaj MD,Zhang S,Harada JJ,Lemaux PG
    Leafy cotyledon genes are essential for induction of somatic embryogenesis of Arabidopsis.
    Planta, 2005. 222(6): p. 977-88
    [PMID:16034595]
  12. Santos Mendoza M,Dubreucq B,Miquel M,Caboche M,Lepiniec L
    LEAFY COTYLEDON 2 activation is sufficient to trigger the accumulation of oil and seed specific mRNAs in Arabidopsis leaves.
    FEBS Lett., 2005. 579(21): p. 4666-70
    [PMID:16107256]
  13. Braybrook SA, et al.
    Genes directly regulated by LEAFY COTYLEDON2 provide insight into the control of embryo maturation and somatic embryogenesis.
    Proc. Natl. Acad. Sci. U.S.A., 2006. 103(9): p. 3468-73
    [PMID:16492731]
  14. To A, et al.
    A network of local and redundant gene regulation governs Arabidopsis seed maturation.
    Plant Cell, 2006. 18(7): p. 1642-51
    [PMID:16731585]
  15. Casson SA,Lindsey K
    The turnip mutant of Arabidopsis reveals that LEAFY COTYLEDON1 expression mediates the effects of auxin and sugars to promote embryonic cell identity.
    Plant Physiol., 2006. 142(2): p. 526-41
    [PMID:16935993]
  16. Underwood BA,Vanderhaeghen R,Whitford R,Town CD,Hilson P
    Simultaneous high-throughput recombinational cloning of open reading frames in closed and open configurations.
    Plant Biotechnol. J., 2006. 4(3): p. 317-24
    [PMID:17147637]
  17. Suzuki M,Wang HH,McCarty DR
    Repression of the LEAFY COTYLEDON 1/B3 regulatory network in plant embryo development by VP1/ABSCISIC ACID INSENSITIVE 3-LIKE B3 genes.
    Plant Physiol., 2007. 143(2): p. 902-11
    [PMID:17158584]
  18. Cao X, et al.
    Abscisic acid and stress signals induce Viviparous1 expression in seed and vegetative tissues of maize.
    Plant Physiol., 2007. 143(2): p. 720-31
    [PMID:17208960]
  19. Baud S, et al.
    WRINKLED1 specifies the regulatory action of LEAFY COTYLEDON2 towards fatty acid metabolism during seed maturation in Arabidopsis.
    Plant J., 2007. 50(5): p. 825-38
    [PMID:17419836]
  20. Wang H,Guo J,Lambert KN,Lin Y
    Developmental control of Arabidopsis seed oil biosynthesis.
    Planta, 2007. 226(3): p. 773-83
    [PMID:17522888]
  21. Bies-Eth
    Inventory, evolution and expression profiling diversity of the LEA (late embryogenesis abundant) protein gene family in Arabidopsis thaliana.
    Plant Mol. Biol., 2008. 67(1-2): p. 107-24
    [PMID:18265943]
  22. Stone SL, et al.
    Arabidopsis LEAFY COTYLEDON2 induces maturation traits and auxin activity: Implications for somatic embryogenesis.
    Proc. Natl. Acad. Sci. U.S.A., 2008. 105(8): p. 3151-6
    [PMID:18287041]
  23. Thakare D,Tang W,Hill K,Perry SE
    The MADS-domain transcriptional regulator AGAMOUS-LIKE15 promotes somatic embryo development in Arabidopsis and soybean.
    Plant Physiol., 2008. 146(4): p. 1663-72
    [PMID:18305206]
  24. Holdsworth MJ,Bentsink L,Soppe WJ
    Molecular networks regulating Arabidopsis seed maturation, after-ripening, dormancy and germination.
    New Phytol., 2008. 179(1): p. 33-54
    [PMID:18422904]
  25. Santos-Mendoza M, et al.
    Deciphering gene regulatory networks that control seed development and maturation in Arabidopsis.
    Plant J., 2008. 54(4): p. 608-20
    [PMID:18476867]
  26. Mu J, et al.
    LEAFY COTYLEDON1 is a key regulator of fatty acid biosynthesis in Arabidopsis.
    Plant Physiol., 2008. 148(2): p. 1042-54
    [PMID:18689444]
  27. Wang X, et al.
    Overexpression of PGA37/MYB118 and MYB115 promotes vegetative-to-embryonic transition in Arabidopsis.
    Cell Res., 2009. 19(2): p. 224-35
    [PMID:18695688]
  28. Swaminathan K,Peterson K,Jack T
    The plant B3 superfamily.
    Trends Plant Sci., 2008. 13(12): p. 647-55
    [PMID:18986826]
  29. Baud S,Lepiniec L
    Regulation of de novo fatty acid synthesis in maturing oilseeds of Arabidopsis.
    Plant Physiol. Biochem., 2009. 47(6): p. 448-55
    [PMID:19136270]
  30. Gao MJ, et al.
    Repression of seed maturation genes by a trihelix transcriptional repressor in Arabidopsis seedlings.
    Plant Cell, 2009. 21(1): p. 54-71
    [PMID:19155348]
  31. Roschzttardtz H, et al.
    A nuclear gene encoding the iron-sulfur subunit of mitochondrial complex II is regulated by B3 domain transcription factors during seed development in Arabidopsis.
    Plant Physiol., 2009. 150(1): p. 84-95
    [PMID:19261733]
  32. Slocombe SP, et al.
    Oil accumulation in leaves directed by modification of fatty acid breakdown and lipid synthesis pathways.
    Plant Biotechnol. J., 2009. 7(7): p. 694-703
    [PMID:19702756]
  33. Ledwoń A,Gaj MD
    LEAFY COTYLEDON2 gene expression and auxin treatment in relation to embryogenic capacity of Arabidopsis somatic cells.
    Plant Cell Rep., 2009. 28(11): p. 1677-88
    [PMID:19763577]
  34. Zheng Y,Ren N,Wang H,Stromberg AJ,Perry SE
    Global identification of targets of the Arabidopsis MADS domain protein AGAMOUS-Like15.
    Plant Cell, 2009. 21(9): p. 2563-77
    [PMID:19767455]
  35. Che N, et al.
    Efficient LEC2 activation of OLEOSIN expression requires two neighboring RY elements on its promoter.
    Sci. China, C, Life Sci., 2009. 52(9): p. 854-63
    [PMID:19802745]
  36. Andrianov V, et al.
    Tobacco as a production platform for biofuel: overexpression of Arabidopsis DGAT and LEC2 genes increases accumulation and shifts the composition of lipids in green biomass.
    Plant Biotechnol. J., 2010. 8(3): p. 277-87
    [PMID:20051035]
  37. Le BH, et al.
    Global analysis of gene activity during Arabidopsis seed development and identification of seed-specific transcription factors.
    Proc. Natl. Acad. Sci. U.S.A., 2010. 107(18): p. 8063-70
    [PMID:20385809]
  38. Willmann MR,Mehalick AJ,Packer RL,Jenik PD
    MicroRNAs regulate the timing of embryo maturation in Arabidopsis.
    Plant Physiol., 2011. 155(4): p. 1871-84
    [PMID:21330492]
  39. Angeles-N
    Mutation of the transcription factor LEAFY COTYLEDON 2 alters the chemical composition of Arabidopsis seeds, decreasing oil and protein content, while maintaining high levels of starch and sucrose in mature seeds.
    J. Plant Physiol., 2011. 168(16): p. 1891-900
    [PMID:21665323]
  40. Berger N,Dubreucq B,Roudier F,Dubos C,Lepiniec L
    Transcriptional regulation of Arabidopsis LEAFY COTYLEDON2 involves RLE, a cis-element that regulates trimethylation of histone H3 at lysine-27.
    Plant Cell, 2011. 23(11): p. 4065-78
    [PMID:22080598]
  41. Tang X, et al.
    Synergistic repression of the embryonic programme by SET DOMAIN GROUP 8 and EMBRYONIC FLOWER 2 in Arabidopsis seedlings.
    J. Exp. Bot., 2012. 63(3): p. 1391-404
    [PMID:22162868]
  42. Angeles-N
    Regulation of AtSUS2 and AtSUS3 by glucose and the transcription factor LEC2 in different tissues and at different stages of Arabidopsis seed development.
    Plant Mol. Biol., 2012. 78(4-5): p. 377-92
    [PMID:22228409]
  43. Gao MJ, et al.
    ASIL1 is required for proper timing of seed filling in Arabidopsis.
    Plant Signal Behav, 2011. 6(12): p. 1886-8
    [PMID:22231199]
  44. Zhang H,Bishop B,Ringenberg W,Muir WM,Ogas J
    The CHD3 remodeler PICKLE associates with genes enriched for trimethylation of histone H3 lysine 27.
    Plant Physiol., 2012. 159(1): p. 418-32
    [PMID:22452853]
  45. M
    Toward the identification and regulation of the Arabidopsis thaliana ABI3 regulon.
    Nucleic Acids Res., 2012. 40(17): p. 8240-54
    [PMID:22730287]
  46. Tang X, et al.
    MicroRNA-mediated repression of the seed maturation program during vegetative development in Arabidopsis.
    PLoS Genet., 2012. 8(11): p. e1003091
    [PMID:23209442]
  47. Wang F,Perry SE
    Identification of direct targets of FUSCA3, a key regulator of Arabidopsis seed development.
    Plant Physiol., 2013. 161(3): p. 1251-64
    [PMID:23314941]
  48. Li-Beisson Y, et al.
    Acyl-lipid metabolism.
    Arabidopsis Book, 2013. 11: p. e0161
    [PMID:23505340]
  49. W
    LEAFY COTYLEDON2 (LEC2) promotes embryogenic induction in somatic tissues of Arabidopsis, via YUCCA-mediated auxin biosynthesis.
    Planta, 2013. 238(3): p. 425-40
    [PMID:23722561]
  50. Feeney M,Frigerio L,Cui Y,Menassa R
    Following vegetative to embryonic cellular changes in leaves of Arabidopsis overexpressing LEAFY COTYLEDON2.
    Plant Physiol., 2013. 162(4): p. 1881-96
    [PMID:23780897]
  51. 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]
  52. Roscoe TT,Guilleminot J,Bessoule JJ,Berger F,Devic M
    Complementation of Seed Maturation Phenotypes by Ectopic Expression of ABSCISIC ACID INSENSITIVE3, FUSCA3 and LEAFY COTYLEDON2 in Arabidopsis.
    Plant Cell Physiol., 2015. 56(6): p. 1215-28
    [PMID:25840088]
  53. Wolkers WF,Alberda M,Koornneef M,L
    Properties of proteins and the glassy matrix in maturation-defective mutant seeds of Arabidopsis thaliana.
    Plant J., 1998. 16(2): p. 133-43
    [PMID:9839460]