RDM3_ARATH
ID RDM3_ARATH Reviewed; 1493 AA.
AC F4JW79;
DT 22-JUL-2015, integrated into UniProtKB/Swiss-Prot.
DT 28-JUN-2011, sequence version 1.
DT 03-AUG-2022, entry version 69.
DE RecName: Full=Protein RNA-directed DNA methylation 3 {ECO:0000303|PubMed:19410546};
DE AltName: Full=KOW domain-containing transcription factor 1 {ECO:0000303|PubMed:19410546};
DE AltName: Full=Protein SPT5-like {ECO:0000303|PubMed:19343051};
GN Name=RDM3 {ECO:0000303|PubMed:19410546};
GN Synonyms=KTF1 {ECO:0000303|PubMed:19410546},
GN SPT5L {ECO:0000303|PubMed:19343051};
GN OrderedLocusNames=At5g04290 {ECO:0000312|Araport:AT5G04290};
GN ORFNames=T19N18.20 {ECO:0000312|EMBL:B61983};
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;
RA Rounsley S.D., Field C.E., Bass S., Linher K., Linher K., Golden K.,
RA Berry K., Granger D., Suh E., Wible C., Adams M.D., Venter J.C.;
RT "A BAC end sequence database for identifying minimal overlaps in
RT Arabidopsis genomic sequencing.";
RL Submitted (NOV-1997) to the EMBL/GenBank/DDBJ databases.
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 FUNCTION, DISRUPTION PHENOTYPE, INTERACTION WITH AGO4 AND RNA TRANSCRIPTS,
RP AND SUBCELLULAR LOCATION.
RC STRAIN=cv. C24, and cv. Columbia;
RX PubMed=19410546; DOI=10.1016/j.cell.2009.04.028;
RA He X.-J., Hsu Y.-F., Zhu S., Wierzbicki A.T., Pontes O., Pikaard C.S.,
RA Liu H.-L., Wang C.-S., Jin H., Zhu J.-K.;
RT "An effector of RNA-directed DNA methylation in arabidopsis is an ARGONAUTE
RT 4- and RNA-binding protein.";
RL Cell 137:498-508(2009).
RN [4]
RP FUNCTION, DISRUPTION PHENOTYPE, AND INTERACTION WITH AGO4.
RC STRAIN=cv. Columbia;
RX PubMed=19343051; DOI=10.1038/embor.2009.31;
RA Bies-Etheve N., Pontier D., Lahmy S., Picart C., Vega D., Cooke R.,
RA Lagrange T.;
RT "RNA-directed DNA methylation requires an AGO4-interacting member of the
RT SPT5 elongation factor family.";
RL EMBO Rep. 10:649-654(2009).
RN [5]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=21150311; DOI=10.4161/epi.6.3.14242;
RA Greenberg M.V., Ausin I., Chan S.W., Cokus S.J., Cuperus J.T., Feng S.,
RA Law J.A., Chu C., Pellegrini M., Carrington J.C., Jacobsen S.E.;
RT "Identification of genes required for de novo DNA methylation in
RT Arabidopsis.";
RL Epigenetics 6:344-354(2011).
RN [6]
RP FUNCTION, INTERACTION WITH CHROMATIN, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. Columbia;
RX PubMed=21738482; DOI=10.1371/journal.pgen.1002120;
RA Rowley M.J., Avrutsky M.I., Sifuentes C.J., Pereira L., Wierzbicki A.T.;
RT "Independent chromatin binding of ARGONAUTE4 and SPT5L/KTF1 mediates
RT transcriptional gene silencing.";
RL PLoS Genet. 7:E1002120-E1002120(2011).
CC -!- FUNCTION: Effector of RNA-directed DNA methylation (RdDM) triggered by
CC small interfering RNAs (siRNAs, 24-nt RNAs). Functions as an adapter
CC protein that binds scaffold transcripts generated by polymerase V and
CC recruits AGO4 and AGO4-bound siRNAs to form an RdDM effector complex
CC (PubMed:19410546, PubMed:19343051). Promotes the expression of 24-nt
CC RNAs (PubMed:19343051). Required for the initial establishment of DNA
CC methylation (PubMed:21150311). Together with AGO4, required for
CC transcriptional gene silencing (TGS) by DNA methylation and repressive
CC histone modifications (H3K9me2) of several chromatin loci
CC (PubMed:21738482). {ECO:0000269|PubMed:19343051,
CC ECO:0000269|PubMed:19410546, ECO:0000269|PubMed:21150311,
CC ECO:0000269|PubMed:21738482}.
CC -!- SUBUNIT: Interacts with AGO4 via its C-terminal region and with RNA
CC transcripts (PubMed:19410546, PubMed:19343051). Binds chromatin at loci
CC subject to transcriptional silencing downstream of RNA Polymerase V,
CC but independently from the presence of 24-nt siRNA (PubMed:21738482).
CC {ECO:0000269|PubMed:19343051, ECO:0000269|PubMed:19410546,
CC ECO:0000269|PubMed:21738482}.
CC -!- INTERACTION:
CC F4JW79; Q9ZVD5: AGO4; NbExp=5; IntAct=EBI-2352225, EBI-2352199;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00768}.
CC Nucleus, nucleoplasm {ECO:0000269|PubMed:19410546}. Note=Localized at
CC punctate nuclear foci. Colocalizes with AGO4 and polymerase V in the
CC nucleoplasm. {ECO:0000269|PubMed:19410546}.
CC -!- DISRUPTION PHENOTYPE: Decrease in the accumulation of several 24-nt
CC RNAs (PubMed:19343051). Reduced DNA methylation and released silencing
CC of RNA-directed DNA methylation (RdDM) target loci promoters (e.g.
CC LTI78/RD29A, YKT61/AtGP1 and AtMU1) without abolishing the siRNA
CC triggers (PubMed:19410546, PubMed:19343051, PubMed:21738482).
CC Suppression of gene silencing mediated by ROS1 disruption in the double
CC mutants ros1 rdm3-1, ros1 rdm3-2 and ros1 rdm3-3 (PubMed:19410546).
CC Loss in non-CG methylation at DRM2-dependent sites (PubMed:21150311).
CC Reduced H3K9me2 at IGN5 and IGN26 loci (PubMed:21738482).
CC {ECO:0000269|PubMed:19343051, ECO:0000269|PubMed:19410546,
CC ECO:0000269|PubMed:21150311, ECO:0000269|PubMed:21738482}.
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DR EMBL; B61983; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; B61984; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CP002688; AED90724.1; -; Genomic_DNA.
DR RefSeq; NP_196049.1; NM_120511.1.
DR AlphaFoldDB; F4JW79; -.
DR SMR; F4JW79; -.
DR IntAct; F4JW79; 2.
DR STRING; 3702.AT5G04290.1; -.
DR iPTMnet; F4JW79; -.
DR PaxDb; F4JW79; -.
DR PRIDE; F4JW79; -.
DR ProteomicsDB; 234905; -.
DR EnsemblPlants; AT5G04290.1; AT5G04290.1; AT5G04290.
DR GeneID; 830308; -.
DR Gramene; AT5G04290.1; AT5G04290.1; AT5G04290.
DR KEGG; ath:AT5G04290; -.
DR Araport; AT5G04290; -.
DR TAIR; locus:2179979; AT5G04290.
DR eggNOG; KOG1999; Eukaryota.
DR HOGENOM; CLU_003564_0_0_1; -.
DR InParanoid; F4JW79; -.
DR OrthoDB; 828863at2759; -.
DR PRO; PR:F4JW79; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; F4JW79; baseline and differential.
DR Genevisible; F4JW79; AT.
DR GO; GO:0032044; C:DSIF complex; IBA:GO_Central.
DR GO; GO:0005654; C:nucleoplasm; IDA:UniProtKB.
DR GO; GO:0003682; F:chromatin binding; IDA:UniProtKB.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0003729; F:mRNA binding; IBA:GO_Central.
DR GO; GO:0003723; F:RNA binding; IDA:UniProtKB.
DR GO; GO:0006306; P:DNA methylation; IMP:UniProtKB.
DR GO; GO:0080188; P:gene silencing by RNA-directed DNA methylation; IMP:UniProtKB.
DR GO; GO:0031507; P:heterochromatin assembly; IMP:UniProtKB.
DR GO; GO:0032784; P:regulation of DNA-templated transcription, elongation; IEA:InterPro.
DR GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR GO; GO:0030422; P:siRNA processing; IMP:TAIR.
DR GO; GO:0006368; P:transcription elongation from RNA polymerase II promoter; IBA:GO_Central.
DR CDD; cd06081; KOW_Spt5_1; 1.
DR CDD; cd06084; KOW_Spt5_4; 1.
DR CDD; cd09888; NGN_Euk; 1.
DR Gene3D; 2.30.30.30; -; 1.
DR Gene3D; 3.30.70.940; -; 1.
DR InterPro; IPR005824; KOW.
DR InterPro; IPR041973; KOW_Spt5_1.
DR InterPro; IPR041977; KOW_Spt5_4.
DR InterPro; IPR005100; NGN-domain.
DR InterPro; IPR036735; NGN_dom_sf.
DR InterPro; IPR039385; NGN_Euk.
DR InterPro; IPR014722; Rib_L2_dom2.
DR InterPro; IPR039659; SPT5.
DR PANTHER; PTHR11125; PTHR11125; 1.
DR Pfam; PF03439; Spt5-NGN; 1.
DR SMART; SM00739; KOW; 3.
PE 1: Evidence at protein level;
KW DNA-binding; Nucleus; Reference proteome; Repeat; RNA-binding;
KW RNA-mediated gene silencing.
FT CHAIN 1..1493
FT /note="Protein RNA-directed DNA methylation 3"
FT /id="PRO_0000433488"
FT DOMAIN 239..266
FT /note="KOW 1"
FT /evidence="ECO:0000255"
FT DOMAIN 501..528
FT /note="KOW 2"
FT /evidence="ECO:0000255"
FT DOMAIN 607..634
FT /note="KOW 3"
FT /evidence="ECO:0000255"
FT REPEAT 732..741
FT /note="1"
FT /evidence="ECO:0000305"
FT REPEAT 775..784
FT /note="2"
FT /evidence="ECO:0000305"
FT REPEAT 789..797
FT /note="3"
FT /evidence="ECO:0000305"
FT REPEAT 818..827
FT /note="4"
FT /evidence="ECO:0000305"
FT REPEAT 836..845
FT /note="5"
FT /evidence="ECO:0000305"
FT REPEAT 854..863
FT /note="6"
FT /evidence="ECO:0000305"
FT REPEAT 866..875
FT /note="7"
FT /evidence="ECO:0000305"
FT REPEAT 883..892
FT /note="8"
FT /evidence="ECO:0000305"
FT REPEAT 917..926
FT /note="9"
FT /evidence="ECO:0000305"
FT REPEAT 935..943
FT /note="10"
FT /evidence="ECO:0000305"
FT REPEAT 944..953
FT /note="11"
FT /evidence="ECO:0000305"
FT REPEAT 954..962
FT /note="12"
FT /evidence="ECO:0000305"
FT REPEAT 963..972
FT /note="13"
FT /evidence="ECO:0000305"
FT REPEAT 978..987
FT /note="14"
FT /evidence="ECO:0000305"
FT REPEAT 1003..1012
FT /note="15"
FT /evidence="ECO:0000305"
FT REPEAT 1013..1022
FT /note="16"
FT /evidence="ECO:0000305"
FT REPEAT 1023..1032
FT /note="17"
FT /evidence="ECO:0000305"
FT REPEAT 1033..1042
FT /note="18"
FT /evidence="ECO:0000305"
FT REPEAT 1043..1052
FT /note="19"
FT /evidence="ECO:0000305"
FT REPEAT 1053..1062
FT /note="20"
FT /evidence="ECO:0000305"
FT REPEAT 1063..1072
FT /note="21"
FT /evidence="ECO:0000305"
FT REPEAT 1073..1082
FT /note="22"
FT /evidence="ECO:0000305"
FT REPEAT 1132..1141
FT /note="23"
FT /evidence="ECO:0000305"
FT REPEAT 1144..1153
FT /note="24"
FT /evidence="ECO:0000305"
FT REPEAT 1156..1165
FT /note="25"
FT /evidence="ECO:0000305"
FT REPEAT 1167..1176
FT /note="26"
FT /evidence="ECO:0000305"
FT REPEAT 1180..1189
FT /note="27"
FT /evidence="ECO:0000305"
FT REPEAT 1192..1201
FT /note="28"
FT /evidence="ECO:0000305"
FT REPEAT 1204..1213
FT /note="29"
FT /evidence="ECO:0000305"
FT REPEAT 1217..1226
FT /note="30"
FT /evidence="ECO:0000305"
FT REPEAT 1229..1238
FT /note="31"
FT /evidence="ECO:0000305"
FT REPEAT 1241..1250
FT /note="32"
FT /evidence="ECO:0000305"
FT REPEAT 1253..1262
FT /note="33"
FT /evidence="ECO:0000305"
FT REPEAT 1266..1275
FT /note="34"
FT /evidence="ECO:0000305"
FT REPEAT 1278..1287
FT /note="35"
FT /evidence="ECO:0000305"
FT REPEAT 1290..1299
FT /note="36"
FT /evidence="ECO:0000305"
FT REPEAT 1302..1311
FT /note="37"
FT /evidence="ECO:0000305"
FT REPEAT 1314..1323
FT /note="38"
FT /evidence="ECO:0000305"
FT REPEAT 1389..1398
FT /note="39"
FT /evidence="ECO:0000305"
FT REPEAT 1433..1442
FT /note="40"
FT /evidence="ECO:0000305"
FT REPEAT 1467..1475
FT /note="41"
FT /evidence="ECO:0000305"
FT REPEAT 1484..1493
FT /note="42"
FT /evidence="ECO:0000305"
FT REGION 1..34
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 54..96
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 393..432
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 578..602
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 692..711
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 728..747
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 732..1493
FT /note="42 X 9 AA approximate WG/GW-rich tandem repeats"
FT /evidence="ECO:0000305"
FT REGION 757..1493
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 21..28
FT /note="Nuclear localization signal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00768"
FT COMPBIAS 65..79
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 80..96
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 785..831
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 834..857
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 865..904
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 919..936
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 951..1084
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1110..1131
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1154..1202
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1214..1239
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1263..1289
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1356..1381
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1392..1416
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1428..1461
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 1493 AA; 158039 MW; CBF42232AD22572D CRC64;
MDRKGKGKQV AGSDSYSGGQ KRKNSVEFRD EGLRIKKRKN PEVLQFFEES AEVGYYGGSS
DEDDDGLGFL NDMEDEPEVE ESSKAGKGEK GKSSFVFPKE EDLNEEEFDR IMEERYKPGS
GFLRYADDDI KDAIEMDALA PTSKDPPIWK VKCAIGRERR SVFCLMHKFV ELRKIGTKLE
IISVFSVDHV KGFIFIEADK EHDVLEACKS LVGIYATRMV LLPKAETPNL LTVQKKTKKV
SEGTWARVKN GKYKGDLAQI VAVSDTRNKA LIKLIPRIDI QALTQKYGGG VTVQKGQTPA
PRLISSSELE EFRPLIQVRR DRDTGITFEH LDSLMLKDGY LYKKVSLDSI SSWGVIPTKD
ELLKFTPVDR KETGDVEWIS EIYGEERKKK ILPTCREGGK GEGSGGGKGE GSGGGKGEGS
RGGKGEGSSD FKSESSYELY NLVCFSRKDF GLIVGVDDKG DGYKVLKEGI DGPVVVTVGK
KEMQNGPFDS KFTALDLNKK QISVNDVVKI SKGPSEGKQG VVRQVYRGII FLYDESEEEN
GGYFCCKSQS CEKVKLFTEE SNEKTGGFDG TAFEDFVSSP KSPLSPEKEW QPRERYNSSN
QGDIGSTYSI GQKLRIRVGP LKGYLCRVIA LRYSDVTVKL DSQHKIFTVK SEHLAEVRDR
NTVLSTSGDA GTGSFQPFGM LGTESSTGDW AIGAGTSSEG GNWNIGGPST DSHESLNIER
NMVQLCREKN PWGGSKPTSD VSPTVADDNT SAWANAAAEN KPASASDQPG GWNPWGKTPA
SEAGTVSGWG DTSASNVEAS SWEKQGASTS NVADLGSWGT HGGSSGGNKQ DEDSVWGKLC
EASESSQKKE ESSWGKKGGS DGESSWGNKD GNSSASKKDG VSWGQQDKGS DESKGGSAWS
NQCGDFGSGK KKDGSSGWNK SAEDSNANSK GVPDWGQPND GSSWGKKGDG AASWGKKDDG
GSWGKKDDGN KDDGGSSWGK KDDGQKDDGG SSWEKKFDGG SSWGKKDDGG SSWGKKDDGG
SLWGKKDDGG SSWGKEDDGG SLWGKKDDGE SSWGKKDDGE SSWGKKDDGG SSWGKKDEGG
YSEQTFDRGG RGFGGRRGGG RRGGRDQFGR GSSFGNSEDP APWSKPSGGS SWGKQDGDGG
GSSWGKENDA GGGSSWGKQD NGVGSSWGKQ NDGSGGGSSW GKQNDAGGGS SWGKQDSGGD
GSSWGKQDGG GDSGSAWGKQ NNTSGGSSWG KQSDAGGGSS WGKQDGGGGG SSWGKQDGGG
GSGSAWGKQN ETSNGSSWGK QNDSGGGSSW GKQDGGGGGS SWGKQNDGGG GSSWGKQGDG
GSKPWNEHSG GGRGFGERRG GGGFRGGRNQ SGRGGRSFDG GRSSSWKTDN QENTWKSDQS
GGSDWKKGWG EDSNNSKPSG SSAGGCAGNW PSWDTNSKKE TNDKPGDDSK SAWGTSNDQV
NTDNNNDSWN KKPNNDVGTS GEADNAWGGK TNAVAPSPSG SAAWGTGDKK TGW
