PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT4G21750.2
Common NameATML1, F17L22.210
Organism
Arabidopsis thaliana
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 HD-ZIP
Protein Properties Length: 762aa    MW: 83490.1 Da    PI: 5.7192
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
AT4G21750.2genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox60.42.9e-1963118156
                  TT--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS
     Homeobox   1 rrkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakek 56 
                  +++ +++t+ q++eLe++F+++++p+ ++r+eL+++l+L+  qVk+WFqN+R+++k
  AT4G21750.2  63 KKRYHRHTQRQIQELESFFKECPHPDDKQRKELSRELSLEPLQVKFWFQNKRTQMK 118
                  688999***********************************************998 PP
2START2161.3e-672624811206
                  HHHHHHHHHHHHHHHHC-TT-EEEE...EXCCTTEEEEEEESSS......SCEEEEEEEECCSCHHHHHHHHHCCCGGCT-TT-S....EEEEEEEEC CS
        START   1 elaeeaaqelvkkalaeepgWvkss...esengdevlqkfeeskv.....dsgealrasgvvdmvlallveellddkeqWdetla....kaetlevis 86 
                  ela +a++elv++a+ ++p+Wv+s    e++n++e+ ++f+++ +      ++ea+r+s+vv+m++ +l e+l+d++ qW+  +     +a tlev+s
  AT4G21750.2 262 ELAVAAMEELVRMAQTGDPLWVSSDnsvEILNEEEYFRTFPRGIGpkpigLRSEASRESTVVIMNHINLIEILMDVN-QWSSVFCgivsRALTLEVLS 358
                  57899*******************9999**************999********************************.******99999********* PP

                  TT......EEEEEEEEXXTTXX-SSX.EEEEEEEEEEE.TTS-EEEEEEEEE-TTS--.-TTSEE-EESSEEEEEEEECTCEEEEEEEE-EE--SSXX CS
        START  87 sg......galqlmvaelqalsplvp.RdfvfvRyirqlgagdwvivdvSvdseqkppesssvvRaellpSgiliepksnghskvtwvehvdlkgrlp 177
                  +g      galq+m+ae+q++splvp R+ +fvRy++q+++g w++vdvS+ds ++ p    + R++++pSg+li++++ng+skvtwveh+++++r++
  AT4G21750.2 359 TGvagnynGALQVMTAEFQVPSPLVPtRENYFVRYCKQHSDGIWAVVDVSLDSLRPSP----ITRSRRRPSGCLIQELQNGYSKVTWVEHIEVDDRSV 452
                  ********************************************************99....7*********************************** PP

                  HHHHHHHHHHHHHHHHHHHHHHTXXXXXX CS
        START 178 hwllrslvksglaegaktwvatlqrqcek 206
                  h+++++lv++gla+gak+wvatl+rqce+
  AT4G21750.2 453 HNMYKPLVNTGLAFGAKRWVATLDRQCER 481
                  ***************************97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:1.10.10.603.0E-2244118IPR009057Homeodomain-like
SuperFamilySSF466891.59E-1852120IPR009057Homeodomain-like
PROSITE profilePS5007117.00660120IPR001356Homeobox domain
SMARTSM003891.5E-1761124IPR001356Homeobox domain
PfamPF000467.5E-1763118IPR001356Homeobox domain
CDDcd000862.64E-1863121No hitNo description
PROSITE patternPS00027095118IPR017970Homeobox, conserved site
PROSITE profilePS5084845.554253484IPR002913START domain
SuperFamilySSF559611.24E-35255483No hitNo description
CDDcd088752.66E-126257480No hitNo description
SMARTSM002343.8E-81262481IPR002913START domain
PfamPF018527.0E-57263481IPR002913START domain
Gene3DG3DSA:3.30.530.201.2E-5361480IPR023393START-like domain
SuperFamilySSF559613.98E-24501682No hitNo description
SuperFamilySSF559613.98E-24715754No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009845Biological Processseed germination
GO:0009913Biological Processepidermal cell differentiation
GO:0048825Biological Processcotyledon development
GO:0090627Biological Processplant epidermal cell differentiation
GO:0005634Cellular Componentnucleus
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0005515Molecular Functionprotein binding
GO:0008289Molecular Functionlipid binding
GO:0043565Molecular Functionsequence-specific DNA binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000013anatomycauline leaf
PO:0000037anatomyshoot apex
PO:0000230anatomyinflorescence meristem
PO:0000293anatomyguard cell
PO:0002002anatomyembryo basal cell
PO:0005679anatomyepidermis
PO:0006210anatomyprotoderm
PO:0008019anatomyleaf lamina base
PO:0009005anatomyroot
PO:0009006anatomyshoot system
PO:0009009anatomyplant embryo
PO:0009010anatomyseed
PO:0009020anatomymeristem L1 layer
PO:0009025anatomyvascular leaf
PO:0009029anatomystamen
PO:0009030anatomycarpel
PO:0009031anatomysepal
PO:0009032anatomypetal
PO:0009046anatomyflower
PO:0009047anatomystem
PO:0009052anatomyflower pedicel
PO:0020030anatomycotyledon
PO:0020038anatomypetiole
PO:0020100anatomyhypocotyl
PO:0020108anatomysuspensor
PO:0020137anatomyleaf apex
PO:0020148anatomyshoot apical meristem
PO:0025022anatomycollective leaf structure
PO:0025281anatomypollen
PO:0025284anatomyembryo apical cell
PO:0001054developmental stagevascular leaf senescent stage
PO:0001078developmental stageplant embryo cotyledonary stage
PO:0001081developmental stagemature plant embryo stage
PO:0001180developmental stageplant proembryo stage
PO:0001185developmental stageplant embryo globular stage
PO:0004507developmental stageplant embryo bilateral stage
PO:0007064developmental stageLP.12 twelve leaves visible stage
PO:0007095developmental stageLP.08 eight leaves visible stage
PO:0007098developmental stageLP.02 two leaves visible stage
PO:0007103developmental stageLP.10 ten leaves visible stage
PO:0007115developmental stageLP.04 four leaves visible stage
PO:0007123developmental stageLP.06 six leaves visible stage
PO:0007611developmental stagepetal differentiation and expansion stage
PO:0007616developmental stageflowering stage
Sequence ? help Back to Top
Protein Sequence    Length: 762 aa     Download sequence    Send to blast
MYHPNMFESH HHMFDMTPKN SENDLGITGS HEEDFETKSG AEVTMENPLE EELQDPNQRP  60
NKKKRYHRHT QRQIQELESF FKECPHPDDK QRKELSRELS LEPLQVKFWF QNKRTQMKAQ  120
HERHENQILK SENDKLRAEN NRYKDALSNA TCPNCGGPAA IGEMSFDEQH LRIENARLRE  180
EIDRISAIAA KYVGKPLMAN SSSFPQLSSS HHIPSRSLDL EVGNFGNNNN SHTGFVGEMF  240
GSSDILRSVS IPSEADKPMI VELAVAAMEE LVRMAQTGDP LWVSSDNSVE ILNEEEYFRT  300
FPRGIGPKPI GLRSEASRES TVVIMNHINL IEILMDVNQW SSVFCGIVSR ALTLEVLSTG  360
VAGNYNGALQ VMTAEFQVPS PLVPTRENYF VRYCKQHSDG IWAVVDVSLD SLRPSPITRS  420
RRRPSGCLIQ ELQNGYSKVT WVEHIEVDDR SVHNMYKPLV NTGLAFGAKR WVATLDRQCE  480
RLASSMASNI PACDLSVITS PEGRKSMLKL AERMVMSFCT GVGASTAHAW TTLSTTGSDD  540
VRVMTRKSMD DPGRPPGIVL SAATSFWIPV APKRVFDFLR DENSRSEWDI LSNGGLVQEM  600
AHIANGRDPG NSVSLLRVNS GNSGQSNMLI LQESCTDASG SYVIYAPVDI IAMNVVLSGG  660
DPDYVALLPS GFAILPDGSA RGGGGSANAS AGAGVEGGGE GNNLEVVTTT GSCGGSLLTV  720
AFQILVDSVP TAKLSLGSVA TVNSLIKCTV ERIKAALACD GA
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.27060.0flower| seed
Expression -- Microarray ? help Back to Top
Source ID E-value
Genevisible254370_at0.0
Expression AtlasAT4G21750-
AtGenExpressAT4G21750-
ATTED-IIAT4G21750-
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: First expressed in the apical cell after the first asymmetric division of the zygote. Expressed in all proembryo cells until the eight-cell stage, and then restricted to the protoderm in the 16-cell proembryo. Not detected in the torpedo stage, but reappeared later in the L1 layer of the shoot apical meristem in the mature embryo. After germination, the L1 layer-specific expression pattern is maintained in the vegetative shoot apical meristem, inflorescence, floral meristems, and the young floral organ primordia. Finally, expressed in the protoderm of the ovule primordia and integuments and gradually restricted to the endothelium surrounding the embryo sac. {ECO:0000269|PubMed:10571886, ECO:0000269|PubMed:8989876}.
Functional Description ? help Back to Top
Source Description
TAIREncodes a homeobox protein similar to GL2. It is expressed in both the apical and basal daughter cells of the zygote as well as their progeny. Expression is detected starting the two-celled stage of embryo development and is later restricted to the outermost, epidermal cell layer from its inception. Its promoter is highly modular with each region contributing to specific aspects of the gene's spatial and temporal expression. Double mutant analysis with PDF2, another L1-specific gene, suggests that their functions are partially redundant and the absence of both of the genes result in abnormal shoot development.
UniProtProbable transcription factor involved in cell specification and pattern formation during embryogenesis. Binds to the L1 box DNA sequence 5'-TAAATG[CT]A-3'. Plays a role in maintaining the identity of L1 cells, possibly by interacting with their L1 box or other target-gene promoters. Functionally redundant to PDF2. {ECO:0000269|PubMed:11439135, ECO:0000269|PubMed:12505995}.
Function -- GeneRIF ? help Back to Top
  1. A 101 bp fragment that conferred all aspects of ATML1 expression contained known binding sites for homeodomain transcription factors and other regulatory sequences.
    [PMID: 17301085]
  2. ATML1 is a master regulator for shoot epidermis identity.
    [PMID: 23515472]
  3. ACR4 positively affects the expression of ATML1 and PDF2 in seedlings. In contrast, ATML1- and PDF2-containing complexes directly and negatively affect both their own expression and that of ACR4.
    [PMID: 24147836]
  4. ATML1 and its target genes are associated with the initial specification of epidermal cell fate and the maintenance of epidermal cells in later stages.
    [PMID: 24205380]
  5. Upon seed imbibition, increased Gibberellin (GA)levels reduce DELLA protein abundance and release ATML1/PDF2 to activate L1 box gene expression, thus enhancing germination potential.
    [PMID: 24989044]
  6. These results indicate that ATML1 and PDF2 act redundantly as a positive regulator of shoot epidermal cell differentiation and at least one copy of these genes is essential for embryo development.
    [PMID: 25766904]
  7. Induction of epidermis cell identity based on the expression of the homeobox gene ATML1 in mesophyll cells enhanced the level of correlation between ploidy and cell volume to near that of wild-type epidermal cells.
    [PMID: 26903507]
  8. The authors find that ATML1 is expressed in all epidermal cells. However, its level fluctuates in each of these cells. If ATML1 levels surpass a threshold during the G2 phase of the cell cycle, the cell will likely enter a state of endoreduplication and become giant.
    [PMID: 28145865]
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT4G21750.2
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 AT4G27330 (R)
Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source Target Gene (A: Activate/R: Repress)
ATRM AT2G42840(A)
Interaction ? help Back to Top
Source Intact With
BioGRIDAT1G14920
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT4G21750
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK2299700.0AK229970.1 Arabidopsis thaliana mRNA for L1 specific homeobox gene ATML1/ovule-specific homeobox protein A20, complete cds, clone: RAFL22-43-B20.
GenBankAY0911040.0AY091104.1 Arabidopsis thaliana putative L1-specific homeobox gene ATML1/ovule-specific homeobox protein A20 (At4g21750) mRNA, complete cds.
GenBankAY1504910.0AY150491.1 Arabidopsis thaliana putative L1-specific homeobox gene ATML1/ovule-specific homeobox protein A20 (At4g21750) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_001031692.10.0Homeobox-leucine zipper family protein / lipid-binding START domain-containing protein
RefseqNP_001329394.10.0Homeobox-leucine zipper family protein / lipid-binding START domain-containing protein
RefseqNP_001329395.10.0Homeobox-leucine zipper family protein / lipid-binding START domain-containing protein
RefseqNP_193906.20.0Homeobox-leucine zipper family protein / lipid-binding START domain-containing protein
SwissprotQ8RWU40.0ATML1_ARATH; Homeobox-leucine zipper protein MERISTEM L1
TrEMBLA0A178UZ610.0A0A178UZ61_ARATH; ATML1
STRINGAT4G21750.20.0(Arabidopsis thaliana)
Publications ? help Back to Top
  1. Sessions A,Weigel D,Yanofsky MF
    The Arabidopsis thaliana MERISTEM LAYER 1 promoter specifies epidermal expression in meristems and young primordia.
    Plant J., 1999. 20(2): p. 259-63
    [PMID:10571886]
  2. Tavares R,Aubourg S,Lecharny A,Kreis M
    Organization and structural evolution of four multigene families in Arabidopsis thaliana: AtLCAD, AtLGT, AtMYST and AtHD-GL2.
    Plant Mol. Biol., 2000. 42(5): p. 703-17
    [PMID:10809443]
  3. Riechmann JL, et al.
    Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
    Science, 2000. 290(5499): p. 2105-10
    [PMID:11118137]
  4. Abe M,Takahashi T,Komeda Y
    Identification of a cis-regulatory element for L1 layer-specific gene expression, which is targeted by an L1-specific homeodomain protein.
    Plant J., 2001. 26(5): p. 487-94
    [PMID:11439135]
  5. Abe M,Katsumata H,Komeda Y,Takahashi T
    Regulation of shoot epidermal cell differentiation by a pair of homeodomain proteins in Arabidopsis.
    Development, 2003. 130(4): p. 635-43
    [PMID:12505995]
  6. Yamada K, et al.
    Empirical analysis of transcriptional activity in the Arabidopsis genome.
    Science, 2003. 302(5646): p. 842-6
    [PMID:14593172]
  7. Johnson KL,Degnan KA,Ross Walker J,Ingram GC
    AtDEK1 is essential for specification of embryonic epidermal cell fate.
    Plant J., 2005. 44(1): p. 114-27
    [PMID:16167900]
  8. 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
    [PMID:16280546]
  9. Nakamura M, et al.
    Characterization of the class IV homeodomain-Leucine Zipper gene family in Arabidopsis.
    Plant Physiol., 2006. 141(4): p. 1363-75
    [PMID:16778018]
  10. Bemis SM,Torii KU
    Autonomy of cell proliferation and developmental programs during Arabidopsis aboveground organ morphogenesis.
    Dev. Biol., 2007. 304(1): p. 367-81
    [PMID:17258192]
  11. Takada S,Jürgens G
    Transcriptional regulation of epidermal cell fate in the Arabidopsis embryo.
    Development, 2007. 134(6): p. 1141-50
    [PMID:17301085]
  12. Tanaka H, et al.
    Novel receptor-like kinase ALE2 controls shoot development by specifying epidermis in Arabidopsis.
    Development, 2007. 134(9): p. 1643-52
    [PMID:17376810]
  13. Wijeratne AJ, et al.
    Differential gene expression in Arabidopsis wild-type and mutant anthers: insights into anther cell differentiation and regulatory networks.
    Plant J., 2007. 52(1): p. 14-29
    [PMID:17666023]
  14. Gordon SP, et al.
    Pattern formation during de novo assembly of the Arabidopsis shoot meristem.
    Development, 2007. 134(19): p. 3539-48
    [PMID:17827180]
  15. Waters MT,Moylan EC,Langdale JA
    GLK transcription factors regulate chloroplast development in a cell-autonomous manner.
    Plant J., 2008. 56(3): p. 432-44
    [PMID:18643989]
  16. 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]
  17. Zhang F, et al.
    An L1 box binding protein, GbML1, interacts with GbMYB25 to control cotton fibre development.
    J. Exp. Bot., 2010. 61(13): p. 3599-613
    [PMID:20667961]
  18. Roeder AH,Cunha A,Ohno CK,Meyerowitz EM
    Cell cycle regulates cell type in the Arabidopsis sepal.
    Development, 2012. 139(23): p. 4416-27
    [PMID:23095885]
  19. Takada S,Takada N,Yoshida A
    ATML1 promotes epidermal cell differentiation in Arabidopsis shoots.
    Development, 2013. 140(9): p. 1919-23
    [PMID:23515472]
  20. Peterson KM, et al.
    Arabidopsis homeodomain-leucine zipper IV proteins promote stomatal development and ectopically induce stomata beyond the epidermis.
    Development, 2013. 140(9): p. 1924-35
    [PMID:23515473]
  21. Kamata N,Okada H,Komeda Y,Takahashi T
    Mutations in epidermis-specific HD-ZIP IV genes affect floral organ identity in Arabidopsis thaliana.
    Plant J., 2013. 75(3): p. 430-40
    [PMID:23590515]
  22. Takada S,Takada N,Yoshida A
    Induction of epidermal cell fate in Arabidopsis shoots.
    Plant Signal Behav, 2013. 8(11): p. e26236
    [PMID:23989220]
  23. San-Bento R,Farcot E,Galletti R,Creff A,Ingram G
    Epidermal identity is maintained by cell-cell communication via a universally active feedback loop in Arabidopsis thaliana.
    Plant J., 2014. 77(1): p. 46-58
    [PMID:24147836]
  24. Takada S
    Post-embryonic induction of ATML1-SRDX alters the morphology of seedlings.
    PLoS ONE, 2013. 8(10): p. e79312
    [PMID:24205380]
  25. Rombol
    Arabidopsis DELLA and two HD-ZIP transcription factors regulate GA signaling in the epidermis through the L1 box cis-element.
    Plant Cell, 2014. 26(7): p. 2905-19
    [PMID:24989044]
  26. 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]
  27. Ogawa E, et al.
    ATML1 and PDF2 Play a Redundant and Essential Role in Arabidopsis Embryo Development.
    Plant Cell Physiol., 2015. 56(6): p. 1183-92
    [PMID:25766904]
  28. Liang Z,Brown RC,Fletcher JC,Opsahl-Sorteberg HG
    Calpain-Mediated Positional Information Directs Cell Wall Orientation to Sustain Plant Stem Cell Activity, Growth and Development.
    Plant Cell Physiol., 2015. 56(9): p. 1855-66
    [PMID:26220906]
  29. Katagiri Y, et al.
    The coordination of ploidy and cell size differs between cell layers in leaves.
    Development, 2016. 143(7): p. 1120-5
    [PMID:26903507]
  30. Seeliger I, et al.
    The AP2-type transcription factors DORNRÖSCHEN and DORNRÖSCHEN-LIKE promote G1/S transition.
    Mol. Genet. Genomics, 2016. 291(5): p. 1835-49
    [PMID:27277595]
  31. Schwarz EM,Roeder AH
    Transcriptomic Effects of the Cell Cycle Regulator LGO in Arabidopsis Sepals.
    Front Plant Sci, 2016. 7: p. 1744
    [PMID:27920789]
  32. Meyer HM, et al.
    Fluctuations of the transcription factor ATML1 generate the pattern of giant cells in the Arabidopsis sepal.
    Elife, 2018.
    [PMID:28145865]
  33. Lu P,Porat R,Nadeau JA,O'Neill SD
    Identification of a meristem L1 layer-specific gene in Arabidopsis that is expressed during embryonic pattern formation and defines a new class of homeobox genes.
    Plant Cell, 1996. 8(12): p. 2155-68
    [PMID:8989876]