RDR1_ARATH
ID RDR1_ARATH Reviewed; 1107 AA.
AC Q9LQV2; Q8H1K9; Q9ZRX5;
DT 08-FEB-2011, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 131.
DE RecName: Full=RNA-dependent RNA polymerase 1;
DE Short=AtRDRP1;
DE EC=2.7.7.48;
DE AltName: Full=RNA-directed RNA polymerase 1;
GN Name=RDR1; Synonyms=RDRP1; OrderedLocusNames=At1g14790; ORFNames=F10B6.19;
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 [MRNA], FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=12650452; DOI=10.1094/mpmi.2003.16.3.206;
RA Yu D., Fan B., MacFarlane S.A., Chen Z.;
RT "Analysis of the involvement of an inducible Arabidopsis RNA-dependent RNA
RT polymerase in antiviral defense.";
RL Mol. Plant Microbe Interact. 16:206-216(2003).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(2000).
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].
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 (JUL-2006) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 479-991.
RC STRAIN=cv. Columbia; TISSUE=Leaf;
RX PubMed=9836747; DOI=10.2307/3870786;
RA Schiebel W., Pelissier T., Riedel L., Thalmeir S., Schiebel R., Kempe D.,
RA Lottspeich F., Saenger H.L., Wassenegger M.;
RT "Isolation of an RNA-directed RNA polymerase-specific cDNA clone from
RT tomato.";
RL Plant Cell 10:2087-2101(1998).
RN [6]
RP FUNCTION.
RX PubMed=19308254; DOI=10.1371/journal.pone.0004971;
RA Qi X., Bao F.S., Xie Z.;
RT "Small RNA deep sequencing reveals role for Arabidopsis thaliana RNA-
RT dependent RNA polymerases in viral siRNA biogenesis.";
RL PLoS ONE 4:E4971-E4971(2009).
RN [7]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=20190077; DOI=10.1105/tpc.109.073056;
RA Garcia-Ruiz H., Takeda A., Chapman E.J., Sullivan C.M., Fahlgren N.,
RA Brempelis K.J., Carrington J.C.;
RT "Arabidopsis RNA-dependent RNA polymerases and dicer-like proteins in
RT antiviral defense and small interfering RNA biogenesis during turnip mosaic
RT virus infection.";
RL Plant Cell 22:481-496(2010).
RN [8]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=19966292; DOI=10.1073/pnas.0904086107;
RA Wang X.B., Wu Q., Ito T., Cillo F., Li W.X., Chen X., Yu J.L., Ding S.W.;
RT "RNAi-mediated viral immunity requires amplification of virus-derived
RT siRNAs in Arabidopsis thaliana.";
RL Proc. Natl. Acad. Sci. U.S.A. 107:484-489(2010).
CC -!- FUNCTION: RNA-dependent direct polymerase involved in antiviral
CC silencing. Required for the production of some small RNAs (mainly 21
CC and some 22 nucleotides) derived from the crucifer-infecting
CC tobamovirus (TMV-cg). Required for turnip mosaic virus (TuMV) silencing
CC and accumulation of viral siRNAs. Involved in cucumber mosaic virus
CC (CMV) silencing. Required for the biogenesis of viral secondary siRNAs,
CC process that follows the production of primary siRNAs derived from
CC viral RNA replication. Specifically targets the positive-strand of the
CC 3 RNA genomes of CMV and preferentially amplifies the 5'-terminal
CC siRNAs of each viral genomic RNA. Not involved in the production of
CC siRNAs derived from a single-stranded 336-nucleotide satellite RNA of
CC CMV. {ECO:0000269|PubMed:12650452, ECO:0000269|PubMed:19308254,
CC ECO:0000269|PubMed:19966292, ECO:0000269|PubMed:20190077}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate +
CC RNA(n+1); Xref=Rhea:RHEA:21248, Rhea:RHEA-COMP:14527, Rhea:RHEA-
CC COMP:17342, ChEBI:CHEBI:33019, ChEBI:CHEBI:61557, ChEBI:CHEBI:140395;
CC EC=2.7.7.48;
CC -!- INDUCTION: By salicylic acid (SA) and infection by a crucifer-infecting
CC tobamovirus (TMV-cg).
CC -!- DISRUPTION PHENOTYPE: Upon viral infection, increased levels of TMV-cg,
CC tobacco rattle virus (TRV) and CMV genomic viral RNAs. Reduced levels
CC of TMV-cg-derived small RNAs and CMV-derived siRNAs.
CC {ECO:0000269|PubMed:12650452, ECO:0000269|PubMed:19966292,
CC ECO:0000269|PubMed:20190077}.
CC -!- SIMILARITY: Belongs to the RdRP family. {ECO:0000305}.
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DR EMBL; AY148431; AAN64409.1; -; mRNA.
DR EMBL; AC006917; AAF79241.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE29226.1; -; Genomic_DNA.
DR EMBL; AK228731; BAF00633.1; -; mRNA.
DR EMBL; AJ011977; CAA09894.1; -; Genomic_DNA.
DR RefSeq; NP_172932.1; NM_101348.4.
DR AlphaFoldDB; Q9LQV2; -.
DR SMR; Q9LQV2; -.
DR STRING; 3702.AT1G14790.1; -.
DR PaxDb; Q9LQV2; -.
DR PRIDE; Q9LQV2; -.
DR ProteomicsDB; 235102; -.
DR EnsemblPlants; AT1G14790.1; AT1G14790.1; AT1G14790.
DR GeneID; 838044; -.
DR Gramene; AT1G14790.1; AT1G14790.1; AT1G14790.
DR KEGG; ath:AT1G14790; -.
DR Araport; AT1G14790; -.
DR TAIR; locus:2006822; AT1G14790.
DR eggNOG; KOG0988; Eukaryota.
DR HOGENOM; CLU_001366_3_0_1; -.
DR InParanoid; Q9LQV2; -.
DR OMA; HTPHIKH; -.
DR OrthoDB; 63910at2759; -.
DR PhylomeDB; Q9LQV2; -.
DR BRENDA; 2.7.7.48; 399.
DR PRO; PR:Q9LQV2; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q9LQV2; baseline and differential.
DR Genevisible; Q9LQV2; AT.
DR GO; GO:0031380; C:nuclear RNA-directed RNA polymerase complex; IBA:GO_Central.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0003968; F:RNA-directed 5'-3' RNA polymerase activity; IBA:GO_Central.
DR GO; GO:0006952; P:defense response; IEA:UniProtKB-KW.
DR GO; GO:0060148; P:positive regulation of post-transcriptional gene silencing; IMP:TAIR.
DR GO; GO:0009751; P:response to salicylic acid; IEP:TAIR.
DR GO; GO:0009615; P:response to virus; IMP:TAIR.
DR GO; GO:0030422; P:siRNA processing; IMP:CACAO.
DR GO; GO:0010025; P:wax biosynthetic process; IGI:TAIR.
DR InterPro; IPR035979; RBD_domain_sf.
DR InterPro; IPR007855; RNA-dep_RNA_pol_euk-typ.
DR PANTHER; PTHR23079; PTHR23079; 1.
DR Pfam; PF05183; RdRP; 1.
DR SUPFAM; SSF54928; SSF54928; 1.
PE 2: Evidence at transcript level;
KW Nucleotidyltransferase; Plant defense; Reference proteome; RNA-binding;
KW RNA-directed RNA polymerase; RNA-mediated gene silencing; Transferase.
FT CHAIN 1..1107
FT /note="RNA-dependent RNA polymerase 1"
FT /id="PRO_0000404672"
FT CONFLICT 758
FT /note="P -> S (in Ref. 1; AAN64409 and 5; CAA09894)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1107 AA; 126214 MW; F8FF97691FF82187 CRC64;
MGKTIQVFGF PNGVSAEEVK KFLERLTGSG TVYAIKVRQP KKGGPRVYAI VQFTSERHTR
LIITAAAERL YYGRSYLKAF EVEQDIVPKP RASLHTISGL KMFFGCQVST KKFLTLWSAQ
DVCVSFGIGM RKLHFSFSWY QKDYRLELSY ENIWQIDLHS PQGRSSKFLV IQVIGAPKIF
EKEDQPINLL FGIMDFYSDG SDEQWIRTTD FTSSSCIGQS TAFCLELPVH LNVPDFRENF
ANYAEHRASS FLIESGSSYS SNANTLVPVV DPPPGFSLPF EILFKLNTLV QNACLSGPAL
DLDFYRLLNQ KKYDRALIDH CLEKLFHLGE CCYEPAHWLR DEYKKWISKG KLPLSPTISL
DDGLVYMYRV QVTPARVYFS GPEVNVSNRV LRHYSKYINN FLRVSFVDED LEKVRSMDLS
PRSSTQRRTK LYDRIYSVLR DGIVIGDKKF EFLAFSSSQL RENSAWMFAP IDRITAAHIR
AWMGDFDHIR NVAKYAARLG QSFSSSRETL NVRSDEIEVI PDVEIISLGT RYVFSDGIGK
ISAEFARKVA RKCGLTEFSP SAFQIRYGGY KGVVAVDPNS SKKLSLRKSM SKFESENTKL
DVLAWSKYQP CYMNRQLITL LSTLGVTDSV FEKKQREVVD RLDAILTHPL EAHEALGLMA
PGENTNILKA LILCGYKPDA EPFLSMMLQN FRASKLLELR TKTRIFISGG RSMMGCLDET
RTLEYGQVVV QYSDPMRPGR RFIITGPVVV AKNPCLHPGD VRVLQAVNVP ALNHMVDCVV
FPQKGLRPHP NECSGSDLDG DIYFVCWDQE LVPPRTSEPM DYTPEPTQIL DHDVTIEEVE
EYFANYIVND SLGIIANAHT AFADKEPLKA FSDPCIELAK KFSTAVDFPK TGVAAVIPQH
LYVKEYPDFM EKPDKPTYES KNVIGKLFRE VKERAPPLIS IKSFTLDVAS KSYDKDMEVD
GFEEYVDEAF YQKANYDFKL GNLMDYYGIK TEAEILSGGI MRMSKSFTKR RDAESIGRAV
RALRKETLSL FNASEEEENE SAKASAWYHV TYHSSYWGLY NEGLNRDHFL SFAWCVYDKL
VRIKKTNLGR RQRQETLERL DHVLRFG
