RPB9B_ARATH
ID RPB9B_ARATH Reviewed; 114 AA.
AC Q8L5V0;
DT 18-SEP-2013, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2002, sequence version 1.
DT 03-AUG-2022, entry version 122.
DE RecName: Full=DNA-directed RNA polymerases II, IV and V subunit 9B;
GN Name=NRPB9B; Synonyms=NRPD9B, NRPE9B; OrderedLocusNames=At4g16265;
GN ORFNames=FCAALL;
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=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 [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].
RA Quinitio C., Chen H., Kim C.J., Shinn P., Ecker J.R.;
RT "Arabidopsis ORF clones.";
RL Submitted (SEP-2006) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RA Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA Feldmann K.A.;
RT "Full-length cDNA from Arabidopsis thaliana.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN [5]
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 [6]
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).
RN [7]
RP FUNCTION, DISRUPTION PHENOTYPE, AND 3D-STRUCTURE MODELING.
RX PubMed=22550619; DOI=10.1016/j.celrep.2012.01.004;
RA Tan E.H., Blevins T., Ream T.S., Pikaard C.S.;
RT "Functional consequences of subunit diversity in RNA polymerases II and
RT V.";
RL Cell Rep. 1:208-214(2012).
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 II which synthesizes mRNA precursors and
CC many functional non-coding RNAs. Pol II is the central component of the
CC basal RNA polymerase II transcription machinery. It is composed of
CC mobile elements that move relative to each other. Component of RNA
CC polymerases IV and V which mediate short-interfering RNAs (siRNA)
CC accumulation and subsequent RNA-directed DNA methylation-dependent
CC (RdDM) transcriptional gene silencing (TGS) of endogenous repeated
CC sequences, including transposable elements. Required for RNA silencing.
CC {ECO:0000269|PubMed:19110459, ECO:0000269|PubMed:22550619}.
CC -!- SUBUNIT: Component of the RNA polymerase II, IV and V complexes.
CC Interacts with NRPD1. {ECO:0000269|PubMed:19110459,
CC ECO:0000269|PubMed:21811420}.
CC -!- SUBCELLULAR LOCATION: Nucleus, nucleolus
CC {ECO:0000250|UniProtKB:P32529}.
CC -!- DISRUPTION PHENOTYPE: Shorter siliques and ovate leaves with shorter
CC petioles, smaller trichomes, prominent leaf veins and changed cuticular
CC wax coating. Loss of methylation at RdDM target sites. Partially
CC redundant with NRPB9A with respect to Pol II. Nrpb9a and nrpb9b double
CC mutants are embryo lethal. {ECO:0000269|PubMed:22550619}.
CC -!- MISCELLANEOUS: The loss of silencing in nrpb9b mutants is due to a
CC defect in Pol V function, but not at the level of transcription. Pol IV
CC functions are not impaired in nrpb9b mutants and Pol II functions are
CC partially complemented by NRPB9A (PubMed:22550619).
CC {ECO:0000305|PubMed:22550619}.
CC -!- SIMILARITY: Belongs to the archaeal RpoM/eukaryotic RPA12/RPB9/RPC11
CC RNA polymerase family. {ECO:0000305}.
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DR EMBL; AL117321; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CP002687; AEE83723.1; -; Genomic_DNA.
DR EMBL; BT028953; ABI49500.1; -; mRNA.
DR EMBL; AY084946; AAM61507.1; -; mRNA.
DR RefSeq; NP_567490.1; NM_117723.4.
DR AlphaFoldDB; Q8L5V0; -.
DR SMR; Q8L5V0; -.
DR BioGRID; 12615; 22.
DR STRING; 3702.AT4G16265.1; -.
DR PaxDb; Q8L5V0; -.
DR PRIDE; Q8L5V0; -.
DR ProteomicsDB; 228217; -.
DR EnsemblPlants; AT4G16265.1; AT4G16265.1; AT4G16265.
DR GeneID; 827321; -.
DR Gramene; AT4G16265.1; AT4G16265.1; AT4G16265.
DR KEGG; ath:AT4G16265; -.
DR Araport; AT4G16265; -.
DR TAIR; locus:505006478; AT4G16265.
DR eggNOG; KOG2691; Eukaryota.
DR HOGENOM; CLU_093932_0_1_1; -.
DR InParanoid; Q8L5V0; -.
DR OMA; CRDCNNM; -.
DR PhylomeDB; Q8L5V0; -.
DR PRO; PR:Q8L5V0; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q8L5V0; baseline and differential.
DR Genevisible; Q8L5V0; AT.
DR GO; GO:0005730; C:nucleolus; IEA:UniProtKB-SubCell.
DR GO; GO:0005665; C:RNA polymerase II, core complex; IDA:UniProtKB.
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:0003676; F:nucleic acid binding; IEA:InterPro.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0080188; P:gene silencing by RNA-directed DNA methylation; IMP:TAIR.
DR GO; GO:0001193; P:maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter; IBA:GO_Central.
DR GO; GO:0006379; P:mRNA cleavage; IEA:InterPro.
DR GO; GO:0006367; P:transcription initiation from RNA polymerase II promoter; IBA:GO_Central.
DR GO; GO:0006283; P:transcription-coupled nucleotide-excision repair; IBA:GO_Central.
DR CDD; cd10508; Zn-ribbon_RPB9; 1.
DR InterPro; IPR019761; DNA-dir_RNA_pol-M_15_CS.
DR InterPro; IPR001529; DNA-dir_RNA_pol_M/15kDasu.
DR InterPro; IPR012164; Rpa12/Rpb9/Rpc10/TFS.
DR InterPro; IPR034012; Zn_ribbon_RPB9_C.
DR InterPro; IPR001222; Znf_TFIIS.
DR PANTHER; PTHR11239; PTHR11239; 1.
DR Pfam; PF02150; RNA_POL_M_15KD; 1.
DR Pfam; PF01096; TFIIS_C; 1.
DR PIRSF; PIRSF005586; RNApol_RpoM; 1.
DR SMART; SM00661; RPOL9; 1.
DR SMART; SM00440; ZnF_C2C2; 1.
DR PROSITE; PS01030; RNA_POL_M_15KD; 1.
DR PROSITE; PS51133; ZF_TFIIS_2; 1.
PE 1: Evidence at protein level;
KW DNA-directed RNA polymerase; Metal-binding; Nucleus; Reference proteome;
KW Transcription; Zinc; Zinc-finger.
FT CHAIN 1..114
FT /note="DNA-directed RNA polymerases II, IV and V subunit
FT 9B"
FT /id="PRO_0000423337"
FT ZN_FING 72..113
FT /note="TFIIS-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00472"
FT BINDING 76
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00472"
FT BINDING 79
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00472"
FT BINDING 103
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00472"
FT BINDING 108
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00472"
SQ SEQUENCE 114 AA; 13107 MW; FF5D0ADD2977757F CRC64;
MSTMKFCREC NNILYPKEDK EQSILLYACR NCDHQEAADN NCVYRNEVHH SVSEQTQILS
DVASDPTLPR TKAVRCAKCQ HGEAVFFQAT ARGEEGMTLF FVCCNPNCSH RWRE
