ATML1_ARATH
ID ATML1_ARATH Reviewed; 762 AA.
AC Q8RWU4; Q38887; Q9SVS2;
DT 29-APR-2008, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2002, sequence version 1.
DT 03-AUG-2022, entry version 138.
DE RecName: Full=Homeobox-leucine zipper protein MERISTEM L1 {ECO:0000303|PubMed:8989876};
DE AltName: Full=HD-ZIP protein ATML1 {ECO:0000303|PubMed:8989876};
DE AltName: Full=Homeodomain transcription factor ATML1 {ECO:0000303|PubMed:8989876};
GN Name=ATML1 {ECO:0000303|PubMed:8989876};
GN OrderedLocusNames=At4g21750 {ECO:0000312|Araport:AT4G21750};
GN ORFNames=F17L22.210 {ECO:0000312|EMBL:CAB36819.1};
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], AND DEVELOPMENTAL STAGE.
RC STRAIN=cv. Landsberg erecta; TISSUE=Meristem;
RX PubMed=8989876; DOI=10.2307/3870458;
RA Lu P., Porat R., Nadeau J.A., O'Neill S.D.;
RT "Identification of a meristem L1 layer-specific gene in Arabidopsis that is
RT expressed during embryonic pattern formation and defines a new class of
RT homeobox genes.";
RL Plant Cell 8:2155-2168(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617198; DOI=10.1038/47134;
RA Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T.,
RA Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B.,
RA Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M.,
RA de Simone V., Obermaier B., Mache R., Mueller M., Kreis M., Delseny M.,
RA Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D.,
RA Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J.,
RA Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B.,
RA Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J.,
RA Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R.,
RA Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P.,
RA Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S.,
RA Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C.,
RA Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J.,
RA Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S.,
RA Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A.,
RA Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M.,
RA Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D.,
RA Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S.,
RA Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R.,
RA Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M.,
RA Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E.,
RA Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P.,
RA Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K.,
RA Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K.,
RA de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K.,
RA Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M.,
RA Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G.,
RA Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K.,
RA Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
RA Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
RA Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H.,
RA Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B.,
RA Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J.,
RA Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K.,
RA O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N.,
RA Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A.,
RA Martienssen R., McCombie W.R.;
RT "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.";
RL Nature 402:769-777(1999).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP DEVELOPMENTAL STAGE.
RX PubMed=10571886; DOI=10.1046/j.1365-313x.1999.00594.x;
RA Sessions A., Weigel D., Yanofsky M.F.;
RT "The Arabidopsis thaliana MERISTEM LAYER 1 promoter specifies epidermal
RT expression in meristems and young primordia.";
RL Plant J. 20:259-263(1999).
RN [7]
RP FUNCTION.
RX PubMed=11439135; DOI=10.1046/j.1365-313x.2001.01047.x;
RA Abe M., Takahashi T., Komeda Y.;
RT "Identification of a cis-regulatory element for L1 layer-specific gene
RT expression, which is targeted by an L1-specific homeodomain protein.";
RL Plant J. 26:487-494(2001).
RN [8]
RP GENE FAMILY.
RX PubMed=10809443; DOI=10.1023/a:1006368316413;
RA Tavares R., Aubourg S., Lecharny A., Kreis M.;
RT "Organization and structural evolution of four multigene families in
RT Arabidopsis thaliana: AtLCAD, AtLGT, AtMYST and AtHD-GL2.";
RL Plant Mol. Biol. 42:703-717(2000).
RN [9]
RP FUNCTION.
RX PubMed=12505995; DOI=10.1242/dev.00292;
RA Abe M., Katsumata H., Komeda Y., Takahashi T.;
RT "Regulation of shoot epidermal cell differentiation by a pair of
RT homeodomain proteins in Arabidopsis.";
RL Development 130:635-643(2003).
RN [10]
RP GENE FAMILY, AND NOMENCLATURE.
RX PubMed=16778018; DOI=10.1104/pp.106.077388;
RA Nakamura M., Katsumata H., Abe M., Yabe N., Komeda Y., Yamamoto K.T.,
RA Takahashi T.;
RT "Characterization of the class IV homeodomain-leucine zipper gene family in
RT Arabidopsis.";
RL Plant Physiol. 141:1363-1375(2006).
RN [11]
RP FUNCTION, DISRUPTION PHENOTYPE, INDUCTION BY IMBIBITION, AND INTERACTION
RP WITH GAI/RGA2; RGA/RGA1/GRS; RGL2/SCL19 AND PDF2.
RC STRAIN=cv. Columbia, and cv. Landsberg erecta;
RX PubMed=24989044; DOI=10.1105/tpc.114.127647;
RA Rombola-Caldentey B., Rueda-Romero P., Iglesias-Fernandez R., Carbonero P.,
RA Onate-Sanchez L.;
RT "Arabidopsis DELLA and two HD-ZIP transcription factors regulate GA
RT signaling in the epidermis through the L1 box cis-element.";
RL Plant Cell 26:2905-2919(2014).
RN [12]
RP FUNCTION, DISRUPTION PHENOTYPE, AND INTERACTION WITH AIL7/PLT7; ANT; BBM
RP AND AIL1.
RC STRAIN=cv. Columbia;
RX PubMed=25564655; DOI=10.1242/dev.117168;
RA Horstman A., Fukuoka H., Muino J.M., Nitsch L., Guo C., Passarinho P.,
RA Sanchez-Perez G., Immink R., Angenent G., Boutilier K.;
RT "AIL and HDG proteins act antagonistically to control cell proliferation.";
RL Development 142:454-464(2015).
CC -!- FUNCTION: Probable transcription factor involved in cell specification
CC and pattern formation during embryogenesis. Binds to the L1 box DNA
CC sequence 5'-TAAATG[CT]A-3'. Plays a role in maintaining the identity of
CC L1 cells, possibly by interacting with their L1 box or other target-
CC gene promoters; binds to the LIP1 gene promoter and stimulates its
CC expression upon imbibition (PubMed:24989044). Acts as a positive
CC regulator of gibberellins (GAs)-regulated epidermal gene expression
CC (e.g. LIP1, LIP2, LTP1, FDH and PDF1) (PubMed:24989044). Functionally
CC redundant to PDF2 (PubMed:24989044). Seems to promote cell
CC differentiation (PubMed:25564655). {ECO:0000269|PubMed:11439135,
CC ECO:0000269|PubMed:12505995, ECO:0000269|PubMed:24989044,
CC ECO:0000269|PubMed:25564655}.
CC -!- SUBUNIT: Interacts with GAI/RGA2, RGA/RGA1/GRS, RGL2/SCL19 and PDF2
CC (PubMed:24989044). Interacts with AIL7/PLT7, ANT, BBM and AIL1
CC (PubMed:25564655). {ECO:0000269|PubMed:24989044,
CC ECO:0000269|PubMed:25564655}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000305}.
CC -!- DEVELOPMENTAL STAGE: First expressed in the apical cell after the first
CC asymmetric division of the zygote. Expressed in all proembryo cells
CC until the eight-cell stage, and then restricted to the protoderm in the
CC 16-cell proembryo. Not detected in the torpedo stage, but reappeared
CC later in the L1 layer of the shoot apical meristem in the mature
CC embryo. After germination, the L1 layer-specific expression pattern is
CC maintained in the vegetative shoot apical meristem, inflorescence,
CC floral meristems, and the young floral organ primordia. Finally,
CC expressed in the protoderm of the ovule primordia and integuments and
CC gradually restricted to the endothelium surrounding the embryo sac.
CC {ECO:0000269|PubMed:10571886, ECO:0000269|PubMed:8989876}.
CC -!- INDUCTION: Stimulated during seed imbibition (PubMed:24989044). Induced
CC by gibberellins (GAs) and repressed by DELLA proteins in an ATML1- and
CC PDF2-dependent manner (PubMed:24989044). Upon seed imbibition,
CC increased GA levels in the epidermis reduce DELLA proteins (e.g.
CC GAI/RGA2, RGA/RGA1/GRS and RGL2/SCL19) abundance and release, in turn,
CC ATML1 and PDF2 which activate LIP1 expression, thus enhancing
CC germination potential (PubMed:24989044). {ECO:0000269|PubMed:24989044}.
CC -!- DISRUPTION PHENOTYPE: Plants missing both PDF2 and ATML1 have reduced
CC levels of L1 box/ gibberellic acid (GA)-regulated putative targets,
CC including LIP1, LIP2, LTP1, FDH and PDF1, in the presence of GA and
CC during seed germination, thus leading to a delayed germination upon
CC imbibition (PubMed:24989044). In plants missing HDG3, HDG7, HDG11, PDF2
CC and ATML1, increased cell division leading to cell overproliferation
CC (PubMed:25564655). {ECO:0000269|PubMed:24989044,
CC ECO:0000269|PubMed:25564655}.
CC -!- SIMILARITY: Belongs to the HD-ZIP homeobox family. Class IV subfamily.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAB49378.1; Type=Miscellaneous discrepancy; Note=Probable cloning artifact leading to a deletion into the sequence.; Evidence={ECO:0000305};
CC Sequence=CAB36819.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=CAB81282.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; U37589; AAB49378.1; ALT_SEQ; mRNA.
DR EMBL; AL035527; CAB36819.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AL161555; CAB81282.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002687; AEE84498.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE84499.1; -; Genomic_DNA.
DR EMBL; CP002687; ANM67574.1; -; Genomic_DNA.
DR EMBL; CP002687; ANM67575.1; -; Genomic_DNA.
DR EMBL; AY091104; AAM14054.1; -; mRNA.
DR EMBL; AY150491; AAN12908.1; -; mRNA.
DR EMBL; AK229970; BAF01795.1; -; mRNA.
DR PIR; T05850; T05850.
DR RefSeq; NP_001031692.1; NM_001036615.3.
DR RefSeq; NP_001329394.1; NM_001341510.1.
DR RefSeq; NP_001329395.1; NM_001341511.1.
DR RefSeq; NP_193906.2; NM_118295.7.
DR AlphaFoldDB; Q8RWU4; -.
DR SMR; Q8RWU4; -.
DR BioGRID; 13552; 4.
DR STRING; 3702.AT4G21750.2; -.
DR iPTMnet; Q8RWU4; -.
DR PaxDb; Q8RWU4; -.
DR PRIDE; Q8RWU4; -.
DR ProteomicsDB; 246583; -.
DR EnsemblPlants; AT4G21750.1; AT4G21750.1; AT4G21750.
DR EnsemblPlants; AT4G21750.2; AT4G21750.2; AT4G21750.
DR EnsemblPlants; AT4G21750.3; AT4G21750.3; AT4G21750.
DR EnsemblPlants; AT4G21750.4; AT4G21750.4; AT4G21750.
DR GeneID; 828263; -.
DR Gramene; AT4G21750.1; AT4G21750.1; AT4G21750.
DR Gramene; AT4G21750.2; AT4G21750.2; AT4G21750.
DR Gramene; AT4G21750.3; AT4G21750.3; AT4G21750.
DR Gramene; AT4G21750.4; AT4G21750.4; AT4G21750.
DR KEGG; ath:AT4G21750; -.
DR Araport; AT4G21750; -.
DR TAIR; locus:2119048; AT4G21750.
DR eggNOG; ENOG502QU3P; Eukaryota.
DR HOGENOM; CLU_015002_2_1_1; -.
DR InParanoid; Q8RWU4; -.
DR OMA; HIDNTWA; -.
DR OrthoDB; 279393at2759; -.
DR PhylomeDB; Q8RWU4; -.
DR PRO; PR:Q8RWU4; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q8RWU4; baseline and differential.
DR Genevisible; Q8RWU4; AT.
DR GO; GO:0005634; C:nucleus; IDA:TAIR.
DR GO; GO:0003677; F:DNA binding; ISS:TAIR.
DR GO; GO:0003700; F:DNA-binding transcription factor activity; ISS:TAIR.
DR GO; GO:0000981; F:DNA-binding transcription factor activity, RNA polymerase II-specific; IEA:InterPro.
DR GO; GO:0008289; F:lipid binding; IEA:InterPro.
DR GO; GO:0043565; F:sequence-specific DNA binding; IDA:TAIR.
DR GO; GO:0048825; P:cotyledon development; IGI:TAIR.
DR GO; GO:0090627; P:plant epidermal cell differentiation; IMP:TAIR.
DR GO; GO:2000033; P:regulation of seed dormancy process; IEP:UniProtKB.
DR GO; GO:0010029; P:regulation of seed germination; IEP:UniProtKB.
DR GO; GO:0009845; P:seed germination; IMP:TAIR.
DR CDD; cd00086; homeodomain; 1.
DR Gene3D; 3.30.530.20; -; 1.
DR InterPro; IPR042160; GLABRA2/ANL2/PDF2/ATML1-like.
DR InterPro; IPR009057; Homeobox-like_sf.
DR InterPro; IPR017970; Homeobox_CS.
DR InterPro; IPR001356; Homeobox_dom.
DR InterPro; IPR023393; START-like_dom_sf.
DR InterPro; IPR002913; START_lipid-bd_dom.
DR PANTHER; PTHR45654; PTHR45654; 1.
DR Pfam; PF00046; Homeodomain; 1.
DR Pfam; PF01852; START; 1.
DR SMART; SM00389; HOX; 1.
DR SMART; SM00234; START; 1.
DR SUPFAM; SSF46689; SSF46689; 1.
DR PROSITE; PS00027; HOMEOBOX_1; 1.
DR PROSITE; PS50071; HOMEOBOX_2; 1.
DR PROSITE; PS50848; START; 1.
PE 1: Evidence at protein level;
KW Coiled coil; Differentiation; DNA-binding; Homeobox; Nucleus;
KW Reference proteome; Transcription; Transcription regulation.
FT CHAIN 1..762
FT /note="Homeobox-leucine zipper protein MERISTEM L1"
FT /id="PRO_0000331662"
FT DOMAIN 253..484
FT /note="START"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00197"
FT DNA_BIND 62..121
FT /note="Homeobox"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00108"
FT REGION 13..72
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 110..192
FT /evidence="ECO:0000255"
FT COMPBIAS 26..40
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT CONFLICT 362
FT /note="A -> R (in Ref. 1; AAB49378)"
FT /evidence="ECO:0000305"
FT CONFLICT 528
FT /note="H -> D (in Ref. 1; AAB49378)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 762 AA; 83490 MW; B19347189893CD44 CRC64;
MYHPNMFESH HHMFDMTPKN SENDLGITGS HEEDFETKSG AEVTMENPLE EELQDPNQRP
NKKKRYHRHT QRQIQELESF FKECPHPDDK QRKELSRELS LEPLQVKFWF QNKRTQMKAQ
HERHENQILK SENDKLRAEN NRYKDALSNA TCPNCGGPAA IGEMSFDEQH LRIENARLRE
EIDRISAIAA KYVGKPLMAN SSSFPQLSSS HHIPSRSLDL EVGNFGNNNN SHTGFVGEMF
GSSDILRSVS IPSEADKPMI VELAVAAMEE LVRMAQTGDP LWVSSDNSVE ILNEEEYFRT
FPRGIGPKPI GLRSEASRES TVVIMNHINL IEILMDVNQW SSVFCGIVSR ALTLEVLSTG
VAGNYNGALQ VMTAEFQVPS PLVPTRENYF VRYCKQHSDG IWAVVDVSLD SLRPSPITRS
RRRPSGCLIQ ELQNGYSKVT WVEHIEVDDR SVHNMYKPLV NTGLAFGAKR WVATLDRQCE
RLASSMASNI PACDLSVITS PEGRKSMLKL AERMVMSFCT GVGASTAHAW TTLSTTGSDD
VRVMTRKSMD DPGRPPGIVL SAATSFWIPV APKRVFDFLR DENSRSEWDI LSNGGLVQEM
AHIANGRDPG NSVSLLRVNS GNSGQSNMLI LQESCTDASG SYVIYAPVDI IAMNVVLSGG
DPDYVALLPS GFAILPDGSA RGGGGSANAS AGAGVEGGGE GNNLEVVTTT GSCGGSLLTV
AFQILVDSVP TAKLSLGSVA TVNSLIKCTV ERIKAALACD GA
