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RNA-dependent RNA polymerase 2 (AtRDRP2) (EC 2.7.7.48) (Protein SILENCING MOVEMENT DEFICIENT 1) (RNA-directed RNA polymerase 2)

 RDR2_ARATH              Reviewed;        1133 AA.
O82504;
08-FEB-2011, integrated into UniProtKB/Swiss-Prot.
01-NOV-1998, sequence version 1.
20-DEC-2017, entry version 112.
RecName: Full=RNA-dependent RNA polymerase 2;
Short=AtRDRP2;
EC=2.7.7.48;
AltName: Full=Protein SILENCING MOVEMENT DEFICIENT 1;
AltName: Full=RNA-directed RNA polymerase 2;
Name=RDR2; Synonyms=RDRP2, SMD1; OrderedLocusNames=At4g11130;
ORFNames=F2P3.11;
Arabidopsis thaliana (Mouse-ear cress).
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;
Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae;
Arabidopsis.
NCBI_TaxID=3702;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Columbia;
PubMed=10617198; DOI=10.1038/47134;
Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G.,
Pohl T., Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N.,
Harris B., Ansorge W., Brandt P., Grivell L.A., Rieger M.,
Weichselgartner M., de Simone V., Obermaier B., Mache R., Mueller M.,
Kreis M., Delseny M., Puigdomenech P., Watson M., Schmidtheini T.,
Reichert B., Portetelle D., Perez-Alonso M., Boutry M., Bancroft I.,
Vos P., Hoheisel J., Zimmermann W., Wedler H., Ridley P.,
Langham S.-A., McCullagh B., Bilham L., Robben J.,
van der Schueren J., Grymonprez B., Chuang Y.-J., Vandenbussche F.,
Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R., Defoor E.,
Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W.,
Mooijman P., Klein Lankhorst R., Rose M., Hauf J., Koetter P.,
Berneiser S., Hempel S., Feldpausch M., Lamberth S., Van den Daele H.,
De Keyser A., Buysshaert C., Gielen J., Villarroel R., De Clercq R.,
van Montagu M., Rogers J., Cronin A., Quail M.A., Bray-Allen S.,
Clark L., Doggett J., Hall S., Kay M., Lennard N., McLay K., Mayes R.,
Pettett A., Rajandream M.A., Lyne M., Benes V., Rechmann S.,
Borkova D., Bloecker H., Scharfe M., Grimm M., Loehnert T.-H.,
Dose S., de Haan M., Maarse A.C., Schaefer M., Mueller-Auer S.,
Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D., Herzl A.,
Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R.,
Schnabl S., Hiller R., Schmidt W., Lecharny A., Aubourg S.,
Chefdor F., Cooke R., Berger C., Monfort A., Casacuberta E.,
Gibbons T., Weber N., Vandenbol M., Bargues M., Terol J., Torres A.,
Perez-Perez A., Purnelle B., Bent E., Johnson S., Tacon D., Jesse T.,
Heijnen L., Schwarz S., Scholler P., Heber S., Francs P., Bielke C.,
Frishman D., Haase D., Lemcke K., Mewes H.-W., Stocker S.,
Zaccaria P., Bevan M., Wilson R.K., de la Bastide M., Habermann K.,
Parnell L., Dedhia N., Gnoj L., Schutz K., Huang E., Spiegel L.,
Sekhon M., Murray J., Sheet P., Cordes M., Abu-Threideh J.,
Stoneking T., Kalicki J., Graves T., Harmon G., Edwards J.,
Latreille P., Courtney L., Cloud J., Abbott A., Scott K., Johnson D.,
Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D.,
Du H., Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C.,
Antonoiu B., Zidanic M., Strong C., Sun H., Lamar B., Yordan C.,
Ma P., Zhong J., Preston R., Vil D., Shekher M., Matero A., Shah R.,
Swaby I.K., O'Shaughnessy A., Rodriguez M., Hoffman J., Till S.,
Granat S., Shohdy N., Hasegawa A., Hameed A., Lodhi M., Johnson A.,
Chen E., Marra M.A., Martienssen R., McCombie W.R.;
"Sequence and analysis of chromosome 4 of the plant Arabidopsis
thaliana.";
Nature 402:769-777(1999).
[2]
GENOME REANNOTATION.
STRAIN=cv. Columbia;
The Arabidopsis Information Portal (Araport);
Submitted (MAY-2016) to the EMBL/GenBank/DDBJ databases.
[3]
FUNCTION.
PubMed=15024409; DOI=10.1371/journal.pbio.0020104;
Xie Z., Johansen L.K., Gustafson A.M., Kasschau K.D., Lellis A.D.,
Zilberman D., Jacobsen S.E., Carrington J.C.;
"Genetic and functional diversification of small RNA pathways in
plants.";
PLoS Biol. 2:E104-E104(2004).
[4]
FUNCTION.
PubMed=15692015; DOI=10.1126/science.1106910;
Herr A.J., Jensen M.B., Dalmay T., Baulcombe D.C.;
"RNA polymerase IV directs silencing of endogenous DNA.";
Science 308:118-120(2005).
[5]
SUBCELLULAR LOCATION.
PubMed=16839878; DOI=10.1016/j.cell.2006.05.031;
Pontes O., Li C.F., Nunes P.C., Haag J., Ream T., Vitins A.,
Jacobsen S.E., Pikaard C.S.;
"The Arabidopsis chromatin-modifying nuclear siRNA pathway involves a
nucleolar RNA processing center.";
Cell 126:79-92(2006).
[6]
FUNCTION.
PubMed=16798886; DOI=10.1105/tpc.106.042127;
Ronemus M., Vaughn M.W., Martienssen R.A.;
"MicroRNA-targeted and small interfering RNA-mediated mRNA degradation
is regulated by argonaute, dicer, and RNA-dependent RNA polymerase in
Arabidopsis.";
Plant Cell 18:1559-1574(2006).
[7]
FUNCTION, AND DISRUPTION PHENOTYPE.
PubMed=17105345; DOI=10.1371/journal.pbio.0040363;
Chan S.W., Zhang X., Bernatavichute Y.V., Jacobsen S.E.;
"Two-step recruitment of RNA-directed DNA methylation to tandem
repeats.";
PLoS Biol. 4:E363-E363(2006).
[8]
FUNCTION, AND SUBCELLULAR LOCATION.
PubMed=17526749; DOI=10.1105/tpc.107.051540;
Smith L.M., Pontes O., Searle I., Yelina N., Yousafzai F.K.,
Herr A.J., Pikaard C.S., Baulcombe D.C.;
"An SNF2 protein associated with nuclear RNA silencing and the spread
of a silencing signal between cells in Arabidopsis.";
Plant Cell 19:1507-1521(2007).
[9]
FUNCTION.
PubMed=17785412; DOI=10.1073/pnas.0706701104;
Brosnan C.A., Mitter N., Christie M., Smith N.A., Waterhouse P.M.,
Carroll B.J.;
"Nuclear gene silencing directs reception of long-distance mRNA
silencing in Arabidopsis.";
Proc. Natl. Acad. Sci. U.S.A. 104:14741-14746(2007).
[10]
FUNCTION.
PubMed=20548962; DOI=10.1371/journal.pgen.1000986;
Vrbsky J., Akimcheva S., Watson J.M., Turner T.L., Daxinger L.,
Vyskot B., Aufsatz W., Riha K.;
"siRNA-mediated methylation of Arabidopsis telomeres.";
PLoS Genet. 6:E1000986-E1000986(2010).
[11]
FUNCTION, AND DISRUPTION PHENOTYPE.
PubMed=21150311; DOI=10.4161/epi.6.3.14242;
Greenberg M.V., Ausin I., Chan S.W., Cokus S.J., Cuperus J.T.,
Feng S., Law J.A., Chu C., Pellegrini M., Carrington J.C.,
Jacobsen S.E.;
"Identification of genes required for de novo DNA methylation in
Arabidopsis.";
Epigenetics 6:344-354(2011).
[12]
IDENTIFICATION BY MASS SPECTROMETRY, AND INTERACTION WITH NRPD1.
PubMed=21811420; DOI=10.1371/journal.pgen.1002195;
Law J.A., Vashisht A.A., Wohlschlegel J.A., Jacobsen S.E.;
"SHH1, a homeodomain protein required for DNA methylation, as well as
RDR2, RDM4, and chromatin remodeling factors, associate with RNA
polymerase IV.";
PLoS Genet. 7:E1002195-E1002195(2011).
[13]
FUNCTION, AND INTERACTION WITH POL IV COMPLEX.
PubMed=23142082; DOI=10.1016/j.molcel.2012.09.027;
Haag J.R., Ream T.S., Marasco M., Nicora C.D., Norbeck A.D.,
Pasa-Tolic L., Pikaard C.S.;
"In vitro transcription activities of Pol IV, Pol V, and RDR2 reveal
coupling of Pol IV and RDR2 for dsRNA synthesis in plant RNA
silencing.";
Mol. Cell 48:811-818(2012).
[14]
IDENTIFICATION BY MASS SPECTROMETRY, AND INTERACTION WITH SHH1.
PubMed=23637343; DOI=10.1073/pnas.1300585110;
Zhang H., Ma Z.Y., Zeng L., Tanaka K., Zhang C.J., Ma J., Bai G.,
Wang P., Zhang S.W., Liu Z.W., Cai T., Tang K., Liu R., Shi X.,
He X.J., Zhu J.K.;
"DTF1 is a core component of RNA-directed DNA methylation and may
assist in the recruitment of Pol IV.";
Proc. Natl. Acad. Sci. U.S.A. 110:8290-8295(2013).
-!- FUNCTION: RNA-dependent direct polymerase involved in the
production of small interfering RNAs (siRNAs). Required for the
biogenesis of endogenous siRNAs of 24 nucleotide which derive from
heterochromatin and DNA repeats such as transposons or endogenous
gene tandem repeats, such as repeats present in FWA gene. Involved
in transcriptional gene silencing (TGS). Component of the RNA-
directed DNA methylation (RdDM) silencing pathway that utilizes
siRNAs to guide DNA methyltransferases to asymmetric cytosines.
Involved in control of flowering time through RdDM of FWA locus.
Required for reception of long-distance mRNA silencing in the
shoot. Required for the formation of telomeric siRNAs and the RNA-
dependent DNA methylation of asymmetric cytosines in telomeric
(5'-CCCTAAA-3') repeats. {ECO:0000269|PubMed:15024409,
ECO:0000269|PubMed:15692015, ECO:0000269|PubMed:16798886,
ECO:0000269|PubMed:17105345, ECO:0000269|PubMed:17526749,
ECO:0000269|PubMed:17785412, ECO:0000269|PubMed:20548962,
ECO:0000269|PubMed:21150311, ECO:0000269|PubMed:23142082}.
-!- CATALYTIC ACTIVITY: Nucleoside triphosphate + RNA(n) = diphosphate
+ RNA(n+1).
-!- SUBUNIT: Interacts with NRPD1 and SHH1. Associates with Pol IV
complex. {ECO:0000269|PubMed:21811420,
ECO:0000269|PubMed:23142082, ECO:0000269|PubMed:23637343}.
-!- SUBCELLULAR LOCATION: Nucleus, nucleoplasm
{ECO:0000269|PubMed:16839878, ECO:0000269|PubMed:17526749}.
Nucleus, nucleolus {ECO:0000269|PubMed:16839878,
ECO:0000269|PubMed:17526749}. Note=In the nucleolus, localized in
a ring or crescent around the inner periphery and to a distinctive
nucleolar dot. {ECO:0000269|PubMed:16839878,
ECO:0000269|PubMed:17526749}.
-!- DISRUPTION PHENOTYPE: Late flowering and absence of siRNAs derived
from FWA tandem repeat regions. Loss of de novo methylation.
{ECO:0000269|PubMed:17105345, ECO:0000269|PubMed:21150311}.
-!- MISCELLANEOUS: RDR2 is non-functional in the absence of associated
Pol IV. {ECO:0000305|PubMed:23142082}.
-!- SIMILARITY: Belongs to the RdRP family. {ECO:0000305}.
-----------------------------------------------------------------------
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Distributed under the Creative Commons Attribution-NoDerivs License
-----------------------------------------------------------------------
EMBL; AF080120; AAC35535.1; -; Genomic_DNA.
EMBL; AL049876; CAB43048.1; -; Genomic_DNA.
EMBL; AL161531; CAB81214.1; -; Genomic_DNA.
EMBL; CP002687; AEE82976.1; -; Genomic_DNA.
PIR; T01920; T01920.
RefSeq; NP_192851.1; NM_117183.3.
UniGene; At.43417; -.
ProteinModelPortal; O82504; -.
SMR; O82504; -.
BioGrid; 12013; 4.
STRING; 3702.AT4G11130.1; -.
iPTMnet; O82504; -.
PaxDb; O82504; -.
EnsemblPlants; AT4G11130.1; AT4G11130.1; AT4G11130.
GeneID; 826714; -.
Gramene; AT4G11130.1; AT4G11130.1; AT4G11130.
KEGG; ath:AT4G11130; -.
Araport; AT4G11130; -.
TAIR; locus:2136068; AT4G11130.
eggNOG; KOG0988; Eukaryota.
eggNOG; ENOG410XQMQ; LUCA.
HOGENOM; HOG000239464; -.
InParanoid; O82504; -.
KO; K11699; -.
OMA; CYVNREI; -.
OrthoDB; EOG093600NW; -.
PhylomeDB; O82504; -.
BRENDA; 2.7.7.48; 399.
PRO; PR:O82504; -.
Proteomes; UP000006548; Chromosome 4.
ExpressionAtlas; O82504; baseline and differential.
Genevisible; O82504; AT.
GO; GO:0005730; C:nucleolus; IDA:TAIR.
GO; GO:0005654; C:nucleoplasm; IEA:UniProtKB-SubCell.
GO; GO:0005634; C:nucleus; IDA:TAIR.
GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
GO; GO:0003968; F:RNA-directed 5'-3' RNA polymerase activity; IEA:UniProtKB-KW.
GO; GO:0050832; P:defense response to fungus; IMP:TAIR.
GO; GO:0016458; P:gene silencing; IMP:TAIR.
GO; GO:0010495; P:long-distance posttranscriptional gene silencing; IMP:TAIR.
GO; GO:0070919; P:production of siRNA involved in chromatin silencing by small RNA; IMP:CACAO.
GO; GO:0030422; P:production of siRNA involved in RNA interference; IMP:TAIR.
InterPro; IPR007855; RNA-dep_RNA_pol_euk-typ.
PANTHER; PTHR23079; PTHR23079; 1.
Pfam; PF05183; RdRP; 1.
1: Evidence at protein level;
Complete proteome; Nucleotidyltransferase; Nucleus;
Reference proteome; RNA-binding; RNA-directed RNA polymerase;
RNA-mediated gene silencing; Transferase.
CHAIN 1 1133 RNA-dependent RNA polymerase 2.
/FTId=PRO_0000404673.
SEQUENCE 1133 AA; 129325 MW; 32B72C4E429B20B9 CRC64;
MVSETTTNRS TVKISNVPQT IVADELLRFL ELHLGEDTVF ALEIPTTRDN WKPRDFARVQ
FTTLEVKSRA QLLSSQSKLL FKTHNLRLSE AYDDIIPRPV DPRKRLDDIV LTVGFPESDE
KRFCALEKWD GVRCWILTEK RRVEFWVWES GDCYKIEVRF EDIIETLSCC VNGDASEIDA
FLLKLKYGPK VFKRVTVHIA TKFKSDRYRF CKEDFDFMWI RTTDFSGSKS IGTSTCFCLE
VHNGSTMLDI FSGLPYYRED TLSLTYVDGK TFASAAQIVP LLNAAILGLE FPYEILFQLN
ALVHAQKISL FAASDMELIK ILRGMSLETA LVILKKLHQQ SSICYDPVFF VKTQMQSVVK
KMKHSPASAY KRLTEQNIMS CQRAYVTPSK IYLLGPELET ANYVVKNFAE HVSDFMRVTF
VEEDWSKLPA NALSVNSKEG YFVKPSRTNI YNRVLSILGE GITVGPKRFE FLAFSASQLR
GNSVWMFASN EKVKAEDIRE WMGCFRKIRS ISKCAARMGQ LFSASRQTLI VRAQDVEQIP
DIEVTTDGAD YCFSDGIGKI SLAFAKQVAQ KCGLSHVPSA FQIRYGGYKG VIAVDRSSFR
KLSLRDSMLK FDSNNRMLNV TRWTESMPCF LNREIICLLS TLGIEDAMFE AMQAVHLSML
GNMLEDRDAA LNVLQKLSGE NSKNLLVKML LQGYAPSSEP YLSMMLRVHH ESQLSELKSR
CRILVPKGRI LIGCMDEMGI LEYGQVYVRV TLTKAELKSR DQSYFRKIDE ETSVVIGKVV
VTKNPCLHPG DIRVLDAIYE VHFEEKGYLD CIIFPQKGER PHPNECSGGD LDGDQFFVSW
DEKIIPSEMD PPMDYAGSRP RLMDHDVTLE EIHKFFVDYM ISDTLGVIST AHLVHADRDP
EKARSQKCLE LANLHSRAVD FAKTGAPAEM PYALKPREFP DFLERFEKPT YISESVFGKL
YRAVKSSLAQ RKPEAESEDT VAYDVTLEEA GFESFIETAK AHRDMYGEKL TSLMIYYGAA
NEEEILTGIL KTKEMYLARD NRRYGDMKDR ITLSVKDLHK EAMGWFEKSC EDEQQKKKLA
SAWYYVTYNP NHRDEKLTFL SFPWIVGDVL LDIKAENAQR QSVEEKTSGL VSI


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