PDF2_ARATH
ID PDF2_ARATH Reviewed; 743 AA.
AC Q93V99; Q9M0Z0; Q9ZPH7;
DT 29-APR-2008, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2001, sequence version 1.
DT 03-AUG-2022, entry version 144.
DE RecName: Full=Homeobox-leucine zipper protein PROTODERMAL FACTOR 2 {ECO:0000303|PubMed:12505995};
DE AltName: Full=HD-ZIP protein PDF2 {ECO:0000303|PubMed:12505995};
DE AltName: Full=Homeodomain transcription factor PDF2 {ECO:0000303|PubMed:12505995};
GN Name=PDF2 {ECO:0000303|PubMed:12505995};
GN OrderedLocusNames=At4g04890 {ECO:0000312|Araport:AT4G04890};
GN ORFNames=T1J1.3 {ECO:0000312|EMBL:AAD17342.1};
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 [GENOMIC DNA], FUNCTION, AND TISSUE SPECIFICITY.
RC STRAIN=cv. Columbia;
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 [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 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 [6]
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 [7]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. Columbia;
RX PubMed=23590515; DOI=10.1111/tpj.12211;
RA Kamata N., Okada H., Komeda Y., Takahashi T.;
RT "Mutations in epidermis-specific HD-ZIP IV genes affect floral organ
RT identity in Arabidopsis thaliana.";
RL Plant J. 75:430-440(2013).
RN [8]
RP FUNCTION, DISRUPTION PHENOTYPE, INDUCTION BY IMBIBITION, AND INTERACTION
RP WITH GAI/RGA2; RGA/RGA1/GRS; RGL2/SCL19 AND ATML1.
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 [9]
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 that 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 ATML1 (PubMed:24989044). Involved, together with HDG
CC proteins (e.g. HDG1, HDG2, HDG5 and HDG12), in the regulation of flower
CC organs development by promoting the expression of APETALA 3 (AP3) in
CC the epidermis and internal cell layers of developing flowers
CC (PubMed:23590515). Seems to promote cell differentiation
CC (PubMed:25564655). {ECO:0000269|PubMed:12505995,
CC ECO:0000269|PubMed:23590515, ECO:0000269|PubMed:24989044,
CC ECO:0000269|PubMed:25564655}.
CC -!- SUBUNIT: Interacts with GAI/RGA2, RGA/RGA1/GRS, RGL2/SCL19 and ATML1
CC (PubMed:24989044). Binds to 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 -!- TISSUE SPECIFICITY: Specifically expressed in the layer 1 (L1) of shoot
CC meristems. {ECO:0000269|PubMed:12505995}.
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). Double mutants pdf2-1 hdg1-1, pdf2-1
CC hdg2-3, pdf2-1 hdg5-1 and pdf2-1 hdg12-2 exhibit abnormal flowers with
CC sepaloid petals and carpelloid stamens in association with a reduced
CC expression of APETALA 3 (AP3) (PubMed:23590515). In plants missing
CC HDG3, HDG7, HDG11, PDF2 and ATML1, increased cell division leading to
CC cell overproliferation (PubMed:25564655). {ECO:0000269|PubMed:23590515,
CC ECO:0000269|PubMed:24989044, ECO:0000269|PubMed:25564655}.
CC -!- SIMILARITY: Belongs to the HD-ZIP homeobox family. Class IV subfamily.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAD17342.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=CAB81031.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AB056455; BAB58961.1; -; Genomic_DNA.
DR EMBL; AF128393; AAD17342.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AL161502; CAB81031.1; ALT_INIT; Genomic_DNA.
DR EMBL; CP002687; AEE82438.1; -; Genomic_DNA.
DR EMBL; CP002687; ANM67658.1; -; Genomic_DNA.
DR EMBL; AF424560; AAL11554.1; -; mRNA.
DR EMBL; AY062575; AAL32653.1; -; mRNA.
DR EMBL; BT000144; AAN15463.1; -; mRNA.
DR PIR; E85061; E85061.
DR RefSeq; NP_001329475.1; NM_001340517.1.
DR RefSeq; NP_567274.1; NM_116727.4.
DR AlphaFoldDB; Q93V99; -.
DR SMR; Q93V99; -.
DR BioGRID; 11139; 8.
DR IntAct; Q93V99; 3.
DR STRING; 3702.AT4G04890.1; -.
DR iPTMnet; Q93V99; -.
DR PaxDb; Q93V99; -.
DR PRIDE; Q93V99; -.
DR ProteomicsDB; 236380; -.
DR EnsemblPlants; AT4G04890.1; AT4G04890.1; AT4G04890.
DR EnsemblPlants; AT4G04890.2; AT4G04890.2; AT4G04890.
DR GeneID; 825828; -.
DR Gramene; AT4G04890.1; AT4G04890.1; AT4G04890.
DR Gramene; AT4G04890.2; AT4G04890.2; AT4G04890.
DR KEGG; ath:AT4G04890; -.
DR Araport; AT4G04890; -.
DR TAIR; locus:2135368; AT4G04890.
DR eggNOG; ENOG502QU3P; Eukaryota.
DR HOGENOM; CLU_015002_2_1_1; -.
DR InParanoid; Q93V99; -.
DR OMA; LVIMNHV; -.
DR OrthoDB; 279393at2759; -.
DR PhylomeDB; Q93V99; -.
DR PRO; PR:Q93V99; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q93V99; baseline and differential.
DR Genevisible; Q93V99; AT.
DR GO; GO:0005634; C:nucleus; IDA:TAIR.
DR GO; GO:0003677; F:DNA binding; IDA: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:0000976; F:transcription cis-regulatory region binding; IPI:TAIR.
DR GO; GO:0048825; P:cotyledon development; IGI:TAIR.
DR GO; GO:0009913; P:epidermal cell differentiation; IMP:TAIR.
DR GO; GO:0048497; P:maintenance of floral organ identity; IGI: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..743
FT /note="Homeobox-leucine zipper protein PROTODERMAL FACTOR
FT 2"
FT /id="PRO_0000331735"
FT DOMAIN 244..476
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 1..72
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 110..192
FT /evidence="ECO:0000255"
FT COMPBIAS 41..55
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 743 AA; 81530 MW; DF305491CC69EF8C CRC64;
MYHPNMFESH HMFDMTPKST SDNDLGITGS REDDFETKSG TEVTTENPSG EELQDPSQRP
NKKKRYHRHT QRQIQELESF FKECPHPDDK QRKELSRDLN LEPLQVKFWF QNKRTQMKAQ
SERHENQILK SDNDKLRAEN NRYKEALSNA TCPNCGGPAA IGEMSFDEQH LRIENARLRE
EIDRISAIAA KYVGKPLGSS FAPLAIHAPS RSLDLEVGNF GNQTGFVGEM YGTGDILRSV
SIPSETDKPI IVELAVAAME ELVRMAQTGD PLWLSTDNSV EILNEEEYFR TFPRGIGPKP
LGLRSEASRQ SAVVIMNHIN LVEILMDVNQ WSCVFSGIVS RALTLEVLST GVAGNYNGAL
QVMTAEFQVP SPLVPTRENY FVRYCKQHSD GSWAVVDVSL DSLRPSTPIL RTRRRPSGCL
IQELPNGYSK VTWIEHMEVD DRSVHNMYKP LVQSGLAFGA KRWVATLERQ CERLASSMAS
NIPGDLSVIT SPEGRKSMLK LAERMVMSFC SGVGASTAHA WTTMSTTGSD DVRVMTRKSM
DDPGRPPGIV LSAATSFWIP VAPKRVFDFL RDENSRKEWD ILSNGGMVQE MAHIANGHEP
GNCVSLLRVN SGNSSQSNML ILQESCTDAS GSYVIYAPVD IVAMNVVLSG GDPDYVALLP
SGFAILPDGS VGGGDGNQHQ EMVSTTSSGS CGGSLLTVAF QILVDSVPTA KLSLGSVATV
NSLIKCTVER IKAAVSCDVG GGA
