ID   RPE5A_ARATH             Reviewed;         222 AA.
AC   Q9M1J2;
DT   18-SEP-2013, integrated into UniProtKB/Swiss-Prot.
DT   01-OCT-2000, sequence version 1.
DT   25-MAY-2022, entry version 131.
DE   RecName: Full=DNA-directed RNA polymerase V subunit 5A;
GN   Name=NRPE5A; Synonyms=RPB23.7, RPB5b; OrderedLocusNames=At3g57080;
GN   ORFNames=F24I3.160;
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=11130713; DOI=10.1038/35048706;
RA   Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B.,
RA   Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M.,
RA   Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V.,
RA   Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P.,
RA   Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M.,
RA   Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H.,
RA   Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H.,
RA   Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A.,
RA   Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H.,
RA   Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J.,
RA   Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B.,
RA   Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
RA   de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
RA   Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G.,
RA   Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X.,
RA   Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M.,
RA   Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B.,
RA   Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J.,
RA   Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C.,
RA   Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y.,
RA   Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K.,
RA   Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A.,
RA   Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
RA   Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT   "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.";
RL   Nature 408:820-822(2000).
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].
RC   STRAIN=cv. Columbia;
RX   PubMed=11910074; DOI=10.1126/science.1071006;
RA   Seki M., Narusaka M., Kamiya A., Ishida J., Satou M., Sakurai T.,
RA   Nakajima M., Enju A., Akiyama K., Oono Y., Muramatsu M., Hayashizaki Y.,
RA   Kawai J., Carninci P., Itoh M., Ishii Y., Arakawa T., Shibata K.,
RA   Shinagawa A., Shinozaki K.;
RT   "Functional annotation of a full-length Arabidopsis cDNA collection.";
RL   Science 296:141-145(2002).
RN   [4]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
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   NUCLEOTIDE SEQUENCE [MRNA] OF 18-222, AND SUBCELLULAR LOCATION.
RX   PubMed=10231567; DOI=10.1016/s0378-1119(99)00090-6;
RA   Larkin R.M., Hagen G., Guilfoyle T.J.;
RT   "Arabidopsis thaliana RNA polymerase II subunits related to yeast and human
RT   RPB5.";
RL   Gene 231:41-47(1999).
RN   [6]
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   [7]
RP   IDENTIFICATION, SUBUNIT, TISSUE SPECIFICITY, AND DISRUPTION PHENOTYPE.
RX   PubMed=19141635; DOI=10.1073/pnas.0810310106;
RA   Lahmy S., Pontier D., Cavel E., Vega D., El-Shami M., Kanno T.,
RA   Lagrange T.;
RT   "PolV(PolIVb) function in RNA-directed DNA methylation requires the
RT   conserved active site and an additional plant-specific subunit.";
RL   Proc. Natl. Acad. Sci. U.S.A. 106:941-946(2009).
RN   [8]
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).
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 polymerase V involved in RNA-directed DNA methylation-
CC       dependent (RdDM) silencing of endogenous repeated sequences, including
CC       transposable elements. Required for establishment of DNA methylation.
CC       {ECO:0000269|PubMed:19110459, ECO:0000269|PubMed:21150311}.
CC   -!- SUBUNIT: Component of the RNA polymerase V complex.
CC       {ECO:0000269|PubMed:19110459, ECO:0000269|PubMed:19141635}.
CC   -!- INTERACTION:
CC       Q9M1J2; Q5D869: NRPE1; NbExp=2; IntAct=EBI-15751359, EBI-2352263;
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:10231567}.
CC   -!- TISSUE SPECIFICITY: Expressed in roots, leaves, siliques and seeds, and
CC       to a lower level, in flower buds and flowers.
CC       {ECO:0000269|PubMed:19141635}.
CC   -!- DISRUPTION PHENOTYPE: Partial loss of methylation and silencing of RdDM
CC       targets, probably due to the redundancy with NRPE5B.
CC       {ECO:0000269|PubMed:19141635, ECO:0000269|PubMed:21150311}.
CC   -!- SIMILARITY: Belongs to the archaeal Rpo5/eukaryotic RPB5 RNA polymerase
CC       subunit family. {ECO:0000305}.
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DR   EMBL; AL138655; CAB72178.1; -; Genomic_DNA.
DR   EMBL; CP002686; AEE79612.1; -; Genomic_DNA.
DR   EMBL; AK118958; BAC43537.1; -; mRNA.
DR   EMBL; BT005410; AAO63830.1; -; mRNA.
DR   PIR; T47768; T47768.
DR   RefSeq; NP_191267.1; NM_115567.3.
DR   AlphaFoldDB; Q9M1J2; -.
DR   SMR; Q9M1J2; -.
DR   BioGRID; 10191; 2.
DR   DIP; DIP-48680N; -.
DR   IntAct; Q9M1J2; 1.
DR   STRING; 3702.AT3G57080.1; -.
DR   PaxDb; Q9M1J2; -.
DR   PRIDE; Q9M1J2; -.
DR   ProteomicsDB; 228206; -.
DR   EnsemblPlants; AT3G57080.1; AT3G57080.1; AT3G57080.
DR   GeneID; 824875; -.
DR   Gramene; AT3G57080.1; AT3G57080.1; AT3G57080.
DR   KEGG; ath:AT3G57080; -.
DR   Araport; AT3G57080; -.
DR   TAIR; locus:2080650; AT3G57080.
DR   eggNOG; KOG3218; Eukaryota.
DR   HOGENOM; CLU_058320_0_0_1; -.
DR   InParanoid; Q9M1J2; -.
DR   OMA; RALHGQN; -.
DR   OrthoDB; 1255823at2759; -.
DR   PhylomeDB; Q9M1J2; -.
DR   PRO; PR:Q9M1J2; -.
DR   Proteomes; UP000006548; Chromosome 3.
DR   ExpressionAtlas; Q9M1J2; baseline and differential.
DR   Genevisible; Q9M1J2; AT.
DR   GO; GO:0000419; C:RNA polymerase V complex; IDA:UniProtKB.
DR   GO; GO:0003677; F:DNA binding; IEA:InterPro.
DR   GO; GO:0003899; F:DNA-directed 5'-3' RNA polymerase activity; IEA:InterPro.
DR   GO; GO:0006351; P:transcription, DNA-templated; IEA:InterPro.
DR   Gene3D; 3.40.1340.10; -; 1.
DR   Gene3D; 3.90.940.20; -; 1.
DR   InterPro; IPR014381; Arch_Rpo5/euc_Rpb5.
DR   InterPro; IPR005571; RNA_pol_Rpb5_N.
DR   InterPro; IPR036710; RNA_pol_Rpb5_N_sf.
DR   InterPro; IPR000783; RNA_pol_subH/Rpb5_C.
DR   InterPro; IPR035913; RPB5-like_sf.
DR   PANTHER; PTHR10535; PTHR10535; 1.
DR   Pfam; PF01191; RNA_pol_Rpb5_C; 1.
DR   Pfam; PF03871; RNA_pol_Rpb5_N; 1.
DR   PIRSF; PIRSF000747; RPB5; 1.
DR   SUPFAM; SSF53036; SSF53036; 1.
DR   SUPFAM; SSF55287; SSF55287; 1.
PE   1: Evidence at protein level;
KW   Nucleus; Reference proteome.
FT   CHAIN           1..222
FT                   /note="DNA-directed RNA polymerase V subunit 5A"
FT                   /id="PRO_0000423327"
SQ   SEQUENCE   222 AA;  25586 MW;  D1CAAA596E22F747 CRC64;
     MEVKGKETAS VLCLSKYVDL SSEESHRYYL ARRNGLQMLR DRGYEVSDED INLSLHDFRT
     VYGERPDVDR LRISALHRSD STKKVKIVFF GTSMVKVNAI RSVVADILSQ ETITGLILVL
     QNHVTNQALK AIELFSFKVE IFQITDLLVN ITKHSLKPQH QVLNDEEKTT LLKKFSIEEK
     QLPRISKKDA IVRYYGLEKG QVVKVNYRGE LTESHVAFRC VW