EBS_ARATH
ID EBS_ARATH Reviewed; 234 AA.
AC F4JL28; O65462; Q56W44; Q8H1R5;
DT 09-DEC-2015, integrated into UniProtKB/Swiss-Prot.
DT 28-JUN-2011, sequence version 1.
DT 25-MAY-2022, entry version 71.
DE RecName: Full=Chromatin remodeling protein EBS {ECO:0000305};
DE AltName: Full=Protein EARLY BOLTING IN SHORT DAYS {ECO:0000303|PubMed:11340178};
GN Name=EBS {ECO:0000303|PubMed:11340178};
GN OrderedLocusNames=At4g22140 {ECO:0000312|EMBL:AEE84562.1};
GN ORFNames=F1N20.240 {ECO:0000312|EMBL:CAA18117.1};
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 {ECO:0000312|Proteomes:UP000006548};
RN [1]
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 [2]
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 [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
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 (MAR-2005) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 39-234 (ISOFORM 1).
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 FUNCTION, DISRUPTION PHENOTYPE, AND MUTAGENESIS OF PRO-41.
RC STRAIN=cv. Landsberg erecta;
RX PubMed=11340178; DOI=10.2307/3871360;
RA Gomez-Mena C., Pineiro M., Franco-Zorrilla J.M., Salinas J., Coupland G.,
RA Martinez-Zapater J.M.;
RT "early bolting in short days: an Arabidopsis mutation that causes early
RT flowering and partially suppresses the floral phenotype of leafy.";
RL Plant Cell 13:1011-1024(2001).
RN [6]
RP FUNCTION, DISRUPTION PHENOTYPE, MUTAGENESIS OF PRO-41, SUBCELLULAR
RP LOCATION, TISSUE SPECIFICITY, AND DEVELOPMENTAL STAGE.
RC STRAIN=cv. Landsberg erecta;
RX PubMed=12837946; DOI=10.1105/tpc.012153;
RA Pineiro M., Gomez-Mena C., Schaffer R., Martinez-Zapater J.M., Coupland G.;
RT "EARLY BOLTING IN SHORT DAYS is related to chromatin remodeling factors and
RT regulates flowering in Arabidopsis by repressing FT.";
RL Plant Cell 15:1552-1562(2003).
RN [7]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=cv. Columbia;
RX PubMed=19245862; DOI=10.1016/j.jprot.2009.02.004;
RA Jones A.M.E., MacLean D., Studholme D.J., Serna-Sanz A., Andreasson E.,
RA Rathjen J.P., Peck S.C.;
RT "Phosphoproteomic analysis of nuclei-enriched fractions from Arabidopsis
RT thaliana.";
RL J. Proteomics 72:439-451(2009).
RN [8]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19376835; DOI=10.1104/pp.109.138677;
RA Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A.,
RA Grossmann J., Gruissem W., Baginsky S.;
RT "Large-scale Arabidopsis phosphoproteome profiling reveals novel
RT chloroplast kinase substrates and phosphorylation networks.";
RL Plant Physiol. 150:889-903(2009).
RN [9]
RP FUNCTION, MUTAGENESIS OF TRP-170, DISRUPTION PHENOTYPE, INTERACTION WITH
RP HISTONE AND HDA6, TISSUE SPECIFICITY, AND DEVELOPMENTAL STAGE.
RC STRAIN=cv. Columbia, and cv. Landsberg erecta;
RX PubMed=25281686; DOI=10.1105/tpc.114.130781;
RA Lopez-Gonzalez L., Mouriz A., Narro-Diego L., Bustos R.,
RA Martinez-Zapater J.M., Jarillo J.A., Pineiro M.;
RT "Chromatin-dependent repression of the Arabidopsis floral integrator genes
RT involves plant specific PHD-containing proteins.";
RL Plant Cell 26:3922-3938(2014).
CC -!- FUNCTION: Chromatin remodeling factor that binds to methylated histone
CC (e.g. H3K4me2/3) to prevent their acetylation (e.g. H3K9K14Ac), likely
CC by recruiting histone deacetylase (HDAC) complexes, and thus regulating
CC the transcription of target genes (PubMed:25281686). Negative regulator
CC in developmental processes in a gibberellic acid- (GA-) dependent
CC manner, such as germination, flowering induction, and flower organ
CC specification, probably by modulating developmental gene expression
CC (PubMed:11340178, PubMed:25281686). Involved in the chromatin-mediated
CC repression of floral initiation and controls genes regulating flowering
CC (PubMed:25281686). Negatively regulates the expression of the floral
CC integrator FT epigenetically, by preventing high levels of H3
CC acetylation, thus maintaining an inactive chromatin conformation at FT
CC locus (PubMed:25281686, PubMed:12837946). {ECO:0000269|PubMed:11340178,
CC ECO:0000269|PubMed:12837946, ECO:0000269|PubMed:25281686}.
CC -!- SUBUNIT: Recognizes di- and trimethylated histone H3 at lysine 4
CC (H3K4me2 and H3K4me3). Interacts with HDA6.
CC {ECO:0000269|PubMed:25281686}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:12837946}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=F4JL28-1; Sequence=Displayed;
CC Name=2;
CC IsoId=F4JL28-2; Sequence=VSP_057983;
CC -!- TISSUE SPECIFICITY: Expressed ubiquitously, with higher levels in
CC floral buds. {ECO:0000269|PubMed:12837946,
CC ECO:0000269|PubMed:25281686}.
CC -!- DEVELOPMENTAL STAGE: Expressed at all stages of development, from
CC seedlings to adult reproductive phase, throughout the shoot apical
CC meristem and young primordia. {ECO:0000269|PubMed:12837946,
CC ECO:0000269|PubMed:25281686}.
CC -!- DISRUPTION PHENOTYPE: Higher H3K9K14 acetylation in the genomic region
CC of the FT locus leading to an enhanced accumulation (PubMed:25281686,
CC PubMed:12837946). In ebs-2, acceleration of flowering associated with a
CC shorter adult vegetative phase (PubMed:11340178, PubMed:12837946,
CC PubMed:25281686). Other developmental defects include smaller leaves
CC and siliques, reduction in seed dormancy, plant size, and fertility,
CC and partial suppression of LEAFY disruption (e.g. lfy-6) effects
CC (PubMed:11340178, PubMed:25281686). {ECO:0000269|PubMed:11340178,
CC ECO:0000269|PubMed:12837946, ECO:0000269|PubMed:25281686}.
CC -!- SIMILARITY: Belongs to the SHL1/EBS protein family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAA18117.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=CAB79169.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AL022140; CAA18117.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AL161556; CAB79169.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002687; AEE84562.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE84563.1; -; Genomic_DNA.
DR EMBL; CP002687; ANM67164.1; -; Genomic_DNA.
DR EMBL; AK222203; BAD95354.1; -; mRNA.
DR EMBL; AY142507; AAN13058.1; -; mRNA.
DR PIR; C85253; C85253.
DR PIR; T49121; T49121.
DR RefSeq; NP_001031695.1; NM_001036618.3. [F4JL28-2]
DR RefSeq; NP_001320030.1; NM_001341530.1. [F4JL28-1]
DR RefSeq; NP_193945.2; NM_118335.5. [F4JL28-1]
DR PDB; 5Z8L; X-ray; 2.00 A; A=1-234.
DR PDB; 5Z8N; X-ray; 3.10 A; A/B/C=1-199.
DR PDBsum; 5Z8L; -.
DR PDBsum; 5Z8N; -.
DR AlphaFoldDB; F4JL28; -.
DR SMR; F4JL28; -.
DR STRING; 3702.AT4G22140.1; -.
DR iPTMnet; F4JL28; -.
DR PaxDb; F4JL28; -.
DR PRIDE; F4JL28; -.
DR ProteomicsDB; 222048; -. [F4JL28-1]
DR EnsemblPlants; AT4G22140.1; AT4G22140.1; AT4G22140. [F4JL28-1]
DR EnsemblPlants; AT4G22140.2; AT4G22140.2; AT4G22140. [F4JL28-2]
DR EnsemblPlants; AT4G22140.3; AT4G22140.3; AT4G22140. [F4JL28-1]
DR GeneID; 828303; -.
DR Gramene; AT4G22140.1; AT4G22140.1; AT4G22140. [F4JL28-1]
DR Gramene; AT4G22140.2; AT4G22140.2; AT4G22140. [F4JL28-2]
DR Gramene; AT4G22140.3; AT4G22140.3; AT4G22140. [F4JL28-1]
DR KEGG; ath:AT4G22140; -.
DR Araport; AT4G22140; -.
DR TAIR; locus:2120693; AT4G22140.
DR eggNOG; KOG1632; Eukaryota.
DR eggNOG; KOG1886; Eukaryota.
DR InParanoid; F4JL28; -.
DR OMA; EWYHPQC; -.
DR OrthoDB; 1092361at2759; -.
DR PRO; PR:F4JL28; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; F4JL28; baseline and differential.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0003682; F:chromatin binding; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0035064; F:methylated histone binding; IDA:UniProtKB.
DR GO; GO:0000976; F:transcription cis-regulatory region binding; IDA:UniProtKB.
DR GO; GO:0006325; P:chromatin organization; IMP:UniProtKB.
DR GO; GO:0009908; P:flower development; IEA:UniProtKB-KW.
DR GO; GO:0035067; P:negative regulation of histone acetylation; IMP:UniProtKB.
DR GO; GO:0048579; P:negative regulation of long-day photoperiodism, flowering; IMP:UniProtKB.
DR GO; GO:0009791; P:post-embryonic development; IMP:UniProtKB.
DR GO; GO:2000028; P:regulation of photoperiodism, flowering; IMP:UniProtKB.
DR GO; GO:0006355; P:regulation of transcription, DNA-templated; IMP:UniProtKB.
DR GO; GO:0009845; P:seed germination; IMP:TAIR.
DR DisProt; DP02690; -.
DR Gene3D; 2.30.30.490; -; 1.
DR Gene3D; 3.30.40.10; -; 1.
DR InterPro; IPR001025; BAH_dom.
DR InterPro; IPR043151; BAH_sf.
DR InterPro; IPR045205; EBS/SHL-like.
DR InterPro; IPR019786; Zinc_finger_PHD-type_CS.
DR InterPro; IPR011011; Znf_FYVE_PHD.
DR InterPro; IPR001965; Znf_PHD.
DR InterPro; IPR019787; Znf_PHD-finger.
DR InterPro; IPR013083; Znf_RING/FYVE/PHD.
DR PANTHER; PTHR46364:SF13; PTHR46364:SF13; 1.
DR Pfam; PF01426; BAH; 1.
DR Pfam; PF00628; PHD; 1.
DR SMART; SM00439; BAH; 1.
DR SMART; SM00249; PHD; 1.
DR SUPFAM; SSF57903; SSF57903; 1.
DR PROSITE; PS51038; BAH; 1.
DR PROSITE; PS01359; ZF_PHD_1; 1.
DR PROSITE; PS50016; ZF_PHD_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Alternative splicing; Chromatin regulator; Flowering;
KW Metal-binding; Nucleus; Reference proteome; Transcription;
KW Transcription regulation; Zinc; Zinc-finger.
FT CHAIN 1..234
FT /note="Chromatin remodeling protein EBS"
FT /id="PRO_0000434827"
FT DOMAIN 29..144
FT /note="BAH"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00370"
FT ZN_FING 146..197
FT /note="PHD-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT VAR_SEQ 218..234
FT /note="RLSLFSHLLYRCSITYL -> ETKRRKR (in isoform 2)"
FT /id="VSP_057983"
FT MUTAGEN 41
FT /note="P->L: In ebs-1; early flowering, especially under
FT short-day photoperiods, reduction in seed dormancy, plant
FT size, and fertility, and partial suppression of LEAFY
FT disruption (e.g. lfy-6) effects."
FT /evidence="ECO:0000269|PubMed:11340178,
FT ECO:0000269|PubMed:12837946"
FT MUTAGEN 170
FT /note="W->A: Impaired H3K4me2/3 binding."
FT /evidence="ECO:0000269|PubMed:25281686"
FT STRAND 17..23
FT /evidence="ECO:0007829|PDB:5Z8N"
FT STRAND 30..32
FT /evidence="ECO:0007829|PDB:5Z8N"
FT STRAND 36..39
FT /evidence="ECO:0007829|PDB:5Z8L"
FT STRAND 42..46
FT /evidence="ECO:0007829|PDB:5Z8N"
FT STRAND 49..58
FT /evidence="ECO:0007829|PDB:5Z8L"
FT STRAND 64..72
FT /evidence="ECO:0007829|PDB:5Z8L"
FT HELIX 74..76
FT /evidence="ECO:0007829|PDB:5Z8L"
FT STRAND 77..79
FT /evidence="ECO:0007829|PDB:5Z8L"
FT STRAND 89..100
FT /evidence="ECO:0007829|PDB:5Z8L"
FT HELIX 101..103
FT /evidence="ECO:0007829|PDB:5Z8L"
FT STRAND 104..112
FT /evidence="ECO:0007829|PDB:5Z8L"
FT HELIX 113..117
FT /evidence="ECO:0007829|PDB:5Z8L"
FT STRAND 126..133
FT /evidence="ECO:0007829|PDB:5Z8L"
FT TURN 135..137
FT /evidence="ECO:0007829|PDB:5Z8L"
FT STRAND 140..143
FT /evidence="ECO:0007829|PDB:5Z8L"
FT TURN 149..152
FT /evidence="ECO:0007829|PDB:5Z8L"
FT STRAND 161..163
FT /evidence="ECO:0007829|PDB:5Z8N"
FT TURN 165..167
FT /evidence="ECO:0007829|PDB:5Z8L"
FT HELIX 173..176
FT /evidence="ECO:0007829|PDB:5Z8L"
FT HELIX 180..185
FT /evidence="ECO:0007829|PDB:5Z8L"
FT HELIX 192..194
FT /evidence="ECO:0007829|PDB:5Z8N"
FT HELIX 211..213
FT /evidence="ECO:0007829|PDB:5Z8L"
SQ SEQUENCE 234 AA; 26566 MW; 3552E498E0FDD583 CRC64;
MAKTRPGVAS KIKTGRKELD SYTIKGTNKV VRAGDCVLMR PSDAGKPPYV ARVEKIEADA
RNNVKVHCRW YYRPEESLGG RRQFHGAKEL FLSDHFDVQS AHTIEGKCIV HTFKNYTRLE
NVGAEDYYCR FEYKAATGAF TPDRVAVYCK CEMPYNPDDL MVQCEGCKDW YHPACVGMTI
EEAKKLDHFV CAECSSDDDV KKSQNGFTSS PADDVKVRLS LFSHLLYRCS ITYL
