NRPD4_ARATH
ID NRPD4_ARATH Reviewed; 205 AA.
AC Q6DBA5; F4JKY1; Q9SUL2;
DT 18-SEP-2013, integrated into UniProtKB/Swiss-Prot.
DT 18-SEP-2013, sequence version 2.
DT 03-AUG-2022, entry version 90.
DE RecName: Full=DNA-directed RNA polymerases IV and V subunit 4;
DE AltName: Full=Protein RNA-DIRECTED DNA METHYLATION 2;
DE AltName: Full=RNA polymerase II, Rpb4, core protein;
GN Name=NRPD4; Synonyms=NRPE4, RDM2; OrderedLocusNames=At4g15950;
GN ORFNames=dl4012w;
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 [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=9461215; DOI=10.1038/35140;
RA Bevan M., Bancroft I., Bent E., Love K., Goodman H.M., Dean C.,
RA Bergkamp R., Dirkse W., van Staveren M., Stiekema W., Drost L., Ridley P.,
RA Hudson S.-A., Patel K., Murphy G., Piffanelli P., Wedler H., Wedler E.,
RA Wambutt R., Weitzenegger T., Pohl T., Terryn N., Gielen J., Villarroel R.,
RA De Clercq R., van Montagu M., Lecharny A., Aubourg S., Gy I., Kreis M.,
RA Lao N., Kavanagh T., Hempel S., Kotter P., Entian K.-D., Rieger M.,
RA Schaefer M., Funk B., Mueller-Auer S., Silvey M., James R., Monfort A.,
RA Pons A., Puigdomenech P., Douka A., Voukelatou E., Milioni D.,
RA Hatzopoulos P., Piravandi E., Obermaier B., Hilbert H., Duesterhoeft A.,
RA Moores T., Jones J.D.G., Eneva T., Palme K., Benes V., Rechmann S.,
RA Ansorge W., Cooke R., Berger C., Delseny M., Voet M., Volckaert G.,
RA Mewes H.-W., Klosterman S., Schueller C., Chalwatzis N.;
RT "Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis
RT thaliana.";
RL Nature 391:485-488(1998).
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].
RA Cheuk R., Chen H., Kim C.J., Shinn P., Ecker J.R.;
RT "Arabidopsis ORF clones.";
RL Submitted (JUL-2004) to the EMBL/GenBank/DDBJ databases.
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 (SEP-2004) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP FUNCTION, DISRUPTION PHENOTYPE, INTERACTION WITH NRPD1 AND NRPE1, TISSUE
RP SPECIFICITY, AND SUBCELLULAR LOCATION.
RX PubMed=19204117; DOI=10.1101/gad.1765209;
RA He X.-J., Hsu Y.-F., Pontes O., Zhu J., Lu J., Bressan R.A., Pikaard C.,
RA Wang C.-S., Zhu J.-K.;
RT "NRPD4, a protein related to the RPB4 subunit of RNA polymerase II, is a
RT component of RNA polymerases IV and V and is required for RNA-directed DNA
RT methylation.";
RL Genes Dev. 23:318-330(2009).
RN [7]
RP FUNCTION, IDENTIFICATION BY MASS SPECTROMETRY, SUBUNIT, AND NOMENCLATURE.
RX PubMed=19110459; DOI=10.1016/j.molcel.2008.12.015;
RA Ream T.S., Haag J.R., Wierzbicki A.T., Nicora C.D., Norbeck A.D., Zhu J.K.,
RA Hagen G., Guilfoyle T.J., Pasa-Tolic L., Pikaard C.S.;
RT "Subunit compositions of the RNA-silencing enzymes Pol IV and Pol V reveal
RT their origins as specialized forms of RNA polymerase II.";
RL Mol. Cell 33:192-203(2009).
RN [8]
RP IDENTIFICATION BY MASS SPECTROMETRY, INTERACTION WITH NRPD1, AND SUBUNIT.
RX PubMed=21811420; DOI=10.1371/journal.pgen.1002195;
RA Law J.A., Vashisht A.A., Wohlschlegel J.A., Jacobsen S.E.;
RT "SHH1, a homeodomain protein required for DNA methylation, as well as RDR2,
RT RDM4, and chromatin remodeling factors, associate with RNA polymerase IV.";
RL PLoS Genet. 7:E1002195-E1002195(2011).
CC -!- FUNCTION: DNA-dependent RNA polymerase catalyzes the transcription of
CC DNA into RNA using the four ribonucleoside triphosphates as substrates.
CC Component of RNA polymerases IV and V which mediate short-interfering
CC RNAs (siRNA) accumulation and subsequent RNA-directed DNA methylation-
CC dependent (RdDM) transcriptional gene silencing (TGS) of endogenous
CC repeated sequences, including transposable elements. Required for the
CC de novo DNA methylation directed by the RdDM pathway.
CC {ECO:0000269|PubMed:19110459, ECO:0000269|PubMed:19204117}.
CC -!- SUBUNIT: Component of the RNA polymerase IV and V complexes. Interacts
CC with NRPD1 and NRPE1. {ECO:0000269|PubMed:19110459,
CC ECO:0000269|PubMed:19204117, ECO:0000269|PubMed:21811420}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:19204117}.
CC Note=Detected as small foci dispersed throughout the nucleoplasm.
CC -!- TISSUE SPECIFICITY: Expressed in shoot meristematic region and in root
CC tips. Detected in cotyledons, flowers and young leaves.
CC {ECO:0000269|PubMed:19204117}.
CC -!- DISRUPTION PHENOTYPE: No developmental phenotype, but reduced DNA
CC methylation at RdDM target loci. {ECO:0000269|PubMed:19204117}.
CC -!- SIMILARITY: Belongs to the eukaryotic RPB4 RNA polymerase subunit
CC family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAB46033.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=CAB78637.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; Z97340; CAB46033.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AL161542; CAB78637.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002687; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; BT015117; AAT71989.1; -; mRNA.
DR EMBL; AK176726; BAD44489.1; -; mRNA.
DR PIR; G85176; G85176.
DR AlphaFoldDB; Q6DBA5; -.
DR SMR; Q6DBA5; -.
DR BioGRID; 12571; 2.
DR STRING; 3702.AT4G15950.1; -.
DR PaxDb; Q6DBA5; -.
DR PRIDE; Q6DBA5; -.
DR ProteomicsDB; 250571; -.
DR Araport; AT4G15950; -.
DR TAIR; locus:2129825; AT4G15950.
DR eggNOG; KOG1535; Eukaryota.
DR HOGENOM; CLU_1334872_0_0_1; -.
DR PRO; PR:Q6DBA5; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q6DBA5; baseline and differential.
DR GO; GO:0005634; C:nucleus; IDA:TAIR.
DR GO; GO:0000418; C:RNA polymerase IV complex; IDA:UniProtKB.
DR GO; GO:0000419; C:RNA polymerase V complex; IDA:UniProtKB.
DR GO; GO:0000166; F:nucleotide binding; IEA:InterPro.
DR GO; GO:0010426; P:DNA methylation on cytosine within a CHH sequence; IMP:TAIR.
DR GO; GO:0035194; P:post-transcriptional gene silencing by RNA; IMP:TAIR.
DR Gene3D; 1.20.1250.40; -; 1.
DR InterPro; IPR010997; HRDC-like_sf.
DR InterPro; IPR006590; RNA_pol_Rpb4/RPC9_core.
DR InterPro; IPR045222; Rpb4-like.
DR InterPro; IPR038324; Rpb4/RPC9_sf.
DR PANTHER; PTHR21297; PTHR21297; 1.
DR SMART; SM00657; RPOL4c; 1.
DR SUPFAM; SSF47819; SSF47819; 1.
PE 1: Evidence at protein level;
KW Nucleus; Reference proteome.
FT CHAIN 1..205
FT /note="DNA-directed RNA polymerases IV and V subunit 4"
FT /id="PRO_0000423332"
FT REGION 1..79
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..38
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 43..66
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT CONFLICT 38
FT /note="R -> G (in Ref. 4; AAT71989 and 5; BAD44489)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 205 AA; 22414 MW; 7336ADDD181B252A CRC64;
MSEKGGKGLK SSLKSKDGGK DGSSTKLKKG RKIHFDQRTP PANYKILNVS SDQQPFQSSA
AKCGKSDKPT KSSKNSLHSF ELKDLPENAE CMMDCEAFQI LDGIKGQLVG LSEDPSIKIP
VSYDRALAYV ESCVHYTNPQ SVRKVLEPLK TYGISDGEMC VIANASSESV DEVLAFIPSL
KTKKEVINQP LQDALEELSK LKKSE
