EDM2_ARATH
ID EDM2_ARATH Reviewed; 1297 AA.
AC F4K3G5; Q9FJ71;
DT 04-FEB-2015, integrated into UniProtKB/Swiss-Prot.
DT 28-JUN-2011, sequence version 1.
DT 03-AUG-2022, entry version 80.
DE RecName: Full=Protein ENHANCED DOWNY MILDEW 2 {ECO:0000303|PubMed:23940361};
GN Name=EDM2 {ECO:0000303|PubMed:23940361};
GN OrderedLocusNames=At5g55390 {ECO:0000312|Araport:AT5G55390};
GN ORFNames=MTE17.10 {ECO:0000312|EMBL:BAB08556.1};
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], FUNCTION, AND DEVELOPMENTAL STAGE.
RC STRAIN=cv. Columbia, and cv. Koch-1;
RX PubMed=23940361; DOI=10.1073/pnas.1312545110;
RA Tsuchiya T., Eulgem T.;
RT "An alternative polyadenylation mechanism coopted to the Arabidopsis RPP7
RT gene through intronic retrotransposon domestication.";
RL Proc. Natl. Acad. Sci. U.S.A. 110:E3535-E3543(2013).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=9872454; DOI=10.1093/dnares/5.5.297;
RA Nakamura Y., Sato S., Asamizu E., Kaneko T., Kotani H., Miyajima N.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. VII. Sequence
RT features of the regions of 1,013,767 bp covered by sixteen physically
RT assigned P1 and TAC clones.";
RL DNA Res. 5:297-308(1998).
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 FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. Columbia;
RX PubMed=17253987; DOI=10.1111/j.1365-313x.2006.02999.x;
RA Eulgem T., Tsuchiya T., Wang X.-J., Beasley B., Cuzick A., Toer M., Zhu T.,
RA McDowell J.M., Holub E., Dangl J.L.;
RT "EDM2 is required for RPP7-dependent disease resistance in Arabidopsis and
RT affects RPP7 transcript levels.";
RL Plant J. 49:829-839(2007).
RN [5]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. Columbia;
RX PubMed=20840782; DOI=10.1186/1471-2229-10-203;
RA Tsuchiya T., Eulgem T.;
RT "Co-option of EDM2 to distinct regulatory modules in Arabidopsis thaliana
RT development.";
RL BMC Plant Biol. 10:203-203(2010).
RN [6]
RP FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH WNK8, AND PHOSPHORYLATION
RP BY WNK8.
RC STRAIN=cv. Columbia;
RX PubMed=20149132; DOI=10.1111/j.1365-313x.2010.04169.x;
RA Tsuchiya T., Eulgem T.;
RT "The Arabidopsis defense component EDM2 affects the floral transition in an
RT FLC-dependent manner.";
RL Plant J. 62:518-528(2010).
RN [7]
RP INTERACTION WITH EML1 AND EML2, SUBCELLULAR LOCATION, AND FUNCTION.
RX PubMed=21830950; DOI=10.1094/mpmi-05-11-0123;
RA Tsuchiya T., Eulgem T.;
RT "EMSY-like genes are required for full RPP7-mediated race-specific immunity
RT and basal defense in Arabidopsis.";
RL Mol. Plant Microbe Interact. 24:1573-1581(2011).
RN [8]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=23976921; DOI=10.1371/journal.pone.0067987;
RA Heidari B., Nemie-Feyissa D., Kangasjarvi S., Lillo C.;
RT "Antagonistic regulation of flowering time through distinct regulatory
RT subunits of protein phosphatase 2A.";
RL PLoS ONE 8:E67987-E67987(2013).
RN [9]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. Columbia;
RX PubMed=23609044; DOI=10.1038/srep01701;
RA Tsuchiya T., Eulgem T.;
RT "Mutations in EDM2 selectively affect silencing states of transposons and
RT induce plant developmental plasticity.";
RL Sci. Rep. 3:1701-1701(2013).
RN [10]
RP DOMAIN PHD.
RX PubMed=25763495; DOI=10.4161/psb.29202;
RA Tsuchiya T., Eulgem T.;
RT "The PHD-finger module of the Arabidopsis thaliana defense regulator EDM2
RT can recognize triply modified histone H3 peptides.";
RL Plant Signal. Behav. 9:E29202-E29202(2014).
RN [11]
RP FUNCTION, DISRUPTION PHENOTYPE, AND DOMAIN PHD.
RC STRAIN=cv. Columbia;
RX PubMed=24248388; DOI=10.1073/pnas.1320106110;
RA Lei M., La H., Lu K., Wang P., Miki D., Ren Z., Duan C.-G., Wang X.,
RA Tang K., Zeng L., Yang L., Zhang H., Nie W., Liu P., Zhou J., Liu R.,
RA Zhong Y., Liu D., Zhu J.K.;
RT "Arabidopsis EDM2 promotes IBM1 distal polyadenylation and regulates genome
RT DNA methylation patterns.";
RL Proc. Natl. Acad. Sci. U.S.A. 111:527-532(2014).
RN [12]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. Columbia;
RX PubMed=27697902; DOI=10.1242/dev.129932;
RA Wang Y., Xue X., Zhu J.-K., Dong J.;
RT "Demethylation of ERECTA receptor genes by IBM1 histone demethylase affects
RT stomatal development.";
RL Development 143:4452-4461(2016).
CC -!- FUNCTION: Cellular antisilencing factor and regulator of genome DNA
CC methylation patterns involved in the regulation of chromatin states.
CC Together with SUVH4, monitors repressive epigenetic marks H3K27me1,
CC H3K9me2, and prevents DNA-methylation at CHG sites, affecting
CC especially the expression of transposons and developmentally important
CC genes (PubMed:21830950, PubMed:23609044, PubMed:24248388). Regulates
CC alternative RNA processing such as distal 3' polyadenylation by
CC intronic heterochromatin (PubMed:24248388). Epigenetic reader that
CC binds DNA and contributes to transcriptional transposable element (TE)
CC silencing by modulating levels of the repressive post-translational
CC histone modifications (PHM) H3K9me2 (PubMed:23609044). In cv. Columbia,
CC required for RPP7-dependent disease resistance against the
CC Hyaloperonospora arabidopsidis isolate Hiks1, by promoting levels of
CC RPP7 via alternative polyadenylation (APA), resulting from cooption of
CC epigenetic information at the TE insertion locus COPIA-R7
CC (PubMed:23940361, PubMed:17253987, PubMed:20149132). Regulates
CC development processes such as the formation of leaf pavement cells,
CC leaf expansion, fertility and flowering (PubMed:20840782,
CC PubMed:20149132, PubMed:23609044). Prevents FLC accumulation to control
CC flowering (PubMed:23976921). Modulates stomatal development by
CC regulating the methylation-mediated silencing of ERECTA receptor genes
CC (e.g. ER, ERL1 and ERL2) and preventing cell divisions
CC (PubMed:27697902). {ECO:0000269|PubMed:17253987,
CC ECO:0000269|PubMed:20149132, ECO:0000269|PubMed:20840782,
CC ECO:0000269|PubMed:21830950, ECO:0000269|PubMed:23609044,
CC ECO:0000269|PubMed:23940361, ECO:0000269|PubMed:23976921,
CC ECO:0000269|PubMed:24248388, ECO:0000269|PubMed:27697902}.
CC -!- SUBUNIT: Interacts with WNK8 in nucleus; this interaction is involved
CC in developmental processes regulation but not in RPP7-dependent disease
CC resistance (PubMed:20149132). Interacts with EML1 and EML2 in nucleus
CC (PubMed:21830950). {ECO:0000269|PubMed:20149132,
CC ECO:0000269|PubMed:21830950}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:20149132,
CC ECO:0000269|PubMed:21830950}.
CC -!- DOMAIN: The PHD domains recognize both active and repressive histone
CC methylation marks at the intronic repeat elements in genes.
CC {ECO:0000269|PubMed:24248388, ECO:0000269|PubMed:25763495}.
CC -!- PTM: Phosphorylated by WNK8. {ECO:0000269|PubMed:20149132}.
CC -!- DISRUPTION PHENOTYPE: Strong reduction in RPP7 levels due to altered
CC H3K9me2 levels in COPIA-R7 (PubMed:23940361, PubMed:17253987). Impaired
CC resistance against the Hyaloperonospora arabidopsidis isolate Hiks1
CC (PubMed:17253987). Abnormal leaf development and flowering time
CC (PubMed:20840782, PubMed:20149132). Enhanced accumulation of FLC
CC (PubMed:23976921). Altered silencing states of several transposons
CC associated with reduced histone methylation at H3K27me1 and H3K9me2
CC (PubMed:23609044). Hypermethylation of DNA at CHG sites
CC (PubMed:24248388). Reduced fertility (PubMed:23609044). Overproduction
CC of stomatal lineage cells due to increased cell divisions and
CC associated with DNA hypermethylation and silencing of ERECTA receptor
CC genes such as ER, ERL1 and ERL2 (PubMed:27697902).
CC {ECO:0000269|PubMed:17253987, ECO:0000269|PubMed:20149132,
CC ECO:0000269|PubMed:20840782, ECO:0000269|PubMed:23609044,
CC ECO:0000269|PubMed:23940361, ECO:0000269|PubMed:23976921,
CC ECO:0000269|PubMed:24248388, ECO:0000269|PubMed:27697902}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAB08556.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; KF112069; AGT37273.1; -; mRNA.
DR EMBL; AB015479; BAB08556.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002688; AED96623.1; -; Genomic_DNA.
DR EMBL; CP002688; AED96624.1; -; Genomic_DNA.
DR EMBL; CP002688; ANM70552.1; -; Genomic_DNA.
DR RefSeq; NP_001190545.1; NM_001203616.2.
DR RefSeq; NP_001332152.1; NM_001345123.1.
DR RefSeq; NP_200350.2; NM_124921.5.
DR AlphaFoldDB; F4K3G5; -.
DR IntAct; F4K3G5; 1.
DR STRING; 3702.AT5G55390.1; -.
DR PaxDb; F4K3G5; -.
DR PRIDE; F4K3G5; -.
DR ProteomicsDB; 247064; -.
DR EnsemblPlants; AT5G55390.1; AT5G55390.1; AT5G55390.
DR EnsemblPlants; AT5G55390.2; AT5G55390.2; AT5G55390.
DR EnsemblPlants; AT5G55390.3; AT5G55390.3; AT5G55390.
DR GeneID; 835632; -.
DR Gramene; AT5G55390.1; AT5G55390.1; AT5G55390.
DR Gramene; AT5G55390.2; AT5G55390.2; AT5G55390.
DR Gramene; AT5G55390.3; AT5G55390.3; AT5G55390.
DR KEGG; ath:AT5G55390; -.
DR Araport; AT5G55390; -.
DR TAIR; locus:2173857; AT5G55390.
DR eggNOG; ENOG502QPIX; Eukaryota.
DR HOGENOM; CLU_003552_2_0_1; -.
DR InParanoid; F4K3G5; -.
DR OMA; FKCASAT; -.
DR OrthoDB; 107088at2759; -.
DR PRO; PR:F4K3G5; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; F4K3G5; baseline and differential.
DR Genevisible; F4K3G5; AT.
DR GO; GO:0000792; C:heterochromatin; IMP:UniProtKB.
DR GO; GO:0005634; C:nucleus; IDA:TAIR.
DR GO; GO:0032991; C:protein-containing complex; IPI:TAIR.
DR GO; GO:0003700; F:DNA-binding transcription factor activity; ISS:TAIR.
DR GO; GO:0140566; F:histone reader activity; IMP:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0043565; F:sequence-specific DNA binding; IDA:UniProtKB.
DR GO; GO:0050832; P:defense response to fungus; IMP:TAIR.
DR GO; GO:0032776; P:DNA methylation on cytosine; IMP:UniProtKB.
DR GO; GO:0090436; P:leaf pavement cell development; IMP:UniProtKB.
DR GO; GO:0009911; P:positive regulation of flower development; IMP:UniProtKB.
DR GO; GO:0061087; P:positive regulation of histone H3-K27 methylation; IMP:UniProtKB.
DR GO; GO:1900111; P:positive regulation of histone H3-K9 dimethylation; IMP:UniProtKB.
DR GO; GO:0044030; P:regulation of DNA methylation; IMP:UniProtKB.
DR GO; GO:0040029; P:regulation of gene expression, epigenetic; IMP:UniProtKB.
DR GO; GO:2000024; P:regulation of leaf development; IMP:UniProtKB.
DR GO; GO:1900363; P:regulation of mRNA polyadenylation; IMP:UniProtKB.
DR GO; GO:0006355; P:regulation of transcription, DNA-templated; IMP:UniProtKB.
DR GO; GO:0007165; P:signal transduction; IMP:TAIR.
DR GO; GO:0010440; P:stomatal lineage progression; IMP:UniProtKB.
DR GO; GO:0010228; P:vegetative to reproductive phase transition of meristem; IMP:UniProtKB.
DR Gene3D; 3.30.40.10; -; 2.
DR InterPro; IPR001965; Znf_PHD.
DR InterPro; IPR013083; Znf_RING/FYVE/PHD.
DR SMART; SM00249; PHD; 3.
PE 1: Evidence at protein level;
KW Chromatin regulator; Developmental protein; DNA-binding; Metal-binding;
KW Nucleus; Phosphoprotein; Plant defense; Reference proteome; Repeat;
KW Transcription; Transcription regulation; Zinc; Zinc-finger.
FT CHAIN 1..1297
FT /note="Protein ENHANCED DOWNY MILDEW 2"
FT /id="PRO_0000431790"
FT ZN_FING 222..281
FT /note="PHD-type 1; degenerate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT ZN_FING 282..352
FT /note="PHD-type 2; atypical"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT ZN_FING 351..417
FT /note="PHD-type 3; degenerate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT REGION 471..547
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 562..598
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 969..1017
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1085..1109
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1260..1297
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 471..493
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 499..547
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 969..993
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 1297 AA; 146788 MW; 69185B6E4B001797 CRC64;
MTFVDDDEEE DFSVPQSASN YYFEDDDKEP VSFARLPIQW SVEEKVDGSG LGFYLRGRSD
NGLLPLHKLV KAWRYDLSNF QPEISVLTKD NIWIKLEEPR KSYGELIRTV LVTLHSIQFL
RRNPQASEKA LWEKLTRSLR SYDVKPSQND LVDHIGLIAE AAKRDRNLAN SKFILAFLTK
KPTKRRLPDE DNAKDDFIVG DEDTYVASDE DELDDEDDDF FESVCAICDN GGEILCCEGS
CLRSFHATKK DGEDSLCDSL GFNKMQVEAI QKYFCPNCEH KIHQCFICKN LGSSDNSSGA
AEVFQCVSAT CGYFYHPHCV TRRLRLGNKE ESEALERQII AGEYTCPLHK CSVCENGEVK
TDSNLQFAVC RRCPKSYHRK CLPREISFED IEDEDILTRA WDGLLHNRVL IYCQEHEIDE
ELLTPVRDHV KFPFTEEQKV FVKEQRRILE SHVGRDKARL KVKDPALQDT CGKASKNSFR
SSFPSSKDGF STKKHGLVSS VPDHSRKRKD IDPSIKHKMV PQKSQKMMED SREAGKNKLG
VKEARDAGKS KISLGERLFS YTQEPNPVKP GRVIPVDSKH NKTDSIASKE PGSEIPTLDN
DSQRRLLAVM KKATEEITMG TILKKFKIQS TMSTHSTRNV VDKTITMGKV EGSVQAIRTA
LKKLEEGGNI EDAKAVCEPE VLSQILKWKD KLKVYLAPFL HGARYTSFGR HFTNPEKLQQ
IVDRLHWYAD DGDMIVDFCC GSNDFSCLMN AKLEETGKKC LYKNYDLFPA KNNFNFERKD
WMTVSKDELE PGSKLIMGLN PPFGVNASLA NKFITKALEF RPKILILIVP PETERLDKKK
SSYVLIWEDK TFLSGNSFYL PGSVNEEDKQ LEDWNLVPPP LSLWSRSDFA AKHKKIAEKH
CHLSRDVGSS KLKIVEEEAN ASLHPLGASD GMCDDIPMEK DELEVAECVN KILVSEKIDT
VETVARVHQS DHLSRRSQLK KEGKTKDYSG RKLGKSMDSN NVDWKSNDME EDQGELSRAP
ESIKVKIPEM TSDWQSPVRS SPDDIYAVCT SISTTTPQRS HEAVEASLPA ITRTKSNLGK
NIREHGCKVQ GTGKPEVSRD RPSSVRTSRE DIYTVRPSPE NTGQKPFEAF EPSYGASLSH
FDDGLAAKYG GFGGGYRMPD PPFLPDQFPL RNGPNEMFDF RGYSDLDRGI GQREYPQQYG
GHLDPMLAPP PPPNLMDNAF PLQQRYAPHF DQMNYQRMSS FPPQPPLQPS GHNLLNPHDF
PLPPPPPSDF EMSPRGFAPG PNPNYPYMSR SGGWIND
