RP6L1_ARATH
ID RP6L1_ARATH Reviewed; 637 AA.
AC Q0WVE8; Q0WMR6; Q9SLI9;
DT 16-SEP-2015, integrated into UniProtKB/Swiss-Prot.
DT 05-SEP-2006, sequence version 1.
DT 03-AUG-2022, entry version 114.
DE RecName: Full=Protein RRP6-like 1 {ECO:0000303|PubMed:18285452};
DE Short=AtRRP6L1 {ECO:0000303|PubMed:18285452};
GN Name=RRP6L1 {ECO:0000303|PubMed:18285452};
GN OrderedLocusNames=At1g54440 {ECO:0000312|Araport:AT1G54440};
GN ORFNames=F20D21.26 {ECO:0000312|EMBL:AAD25623.1};
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, SUBCELLULAR LOCATION, AND DISRUPTION
RP PHENOTYPE.
RC STRAIN=cv. Columbia;
RX PubMed=18285452; DOI=10.1128/mcb.02064-07;
RA Lange H., Holec S., Cognat V., Pieuchot L., Le Ret M., Canaday J.,
RA Gagliardi D.;
RT "Degradation of a polyadenylated rRNA maturation by-product involves one of
RT the three RRP6-like proteins in Arabidopsis thaliana.";
RL Mol. Cell. Biol. 28:3038-3044(2008).
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 FUNCTION.
RX PubMed=23555312; DOI=10.1371/journal.pgen.1003411;
RA Shin J.H., Wang H.L., Lee J., Dinwiddie B.L., Belostotsky D.A.,
RA Chekanova J.A.;
RT "The role of the Arabidopsis Exosome in siRNA-independent silencing of
RT heterochromatic loci.";
RL PLoS Genet. 9:E1003411-E1003411(2013).
RN [6]
RP FUNCTION.
RX PubMed=24726328; DOI=10.1016/j.molcel.2014.03.019;
RA Zhang H., Tang K., Qian W., Duan C.G., Wang B., Zhang H., Wang P., Zhu X.,
RA Lang Z., Yang Y., Zhu J.K.;
RT "An Rrp6-like protein positively regulates noncoding RNA levels and DNA
RT methylation in Arabidopsis.";
RL Mol. Cell 54:418-430(2014).
RN [7]
RP FUNCTION.
RX PubMed=24719467; DOI=10.1093/mp/ssu043;
RA Hsu Y.F., Hsiao Y.C., Wang C.S., Zhan X., Zhang H., Wang C.S.;
RT "AtRRP6L1, a homolog of conserved yeast Exosomal Rrp6p, plays an important
RT role in transcriptional gene silencing in arabidopsis.";
RL Mol. Plant 7:1490-1493(2014).
RN [8]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=25211139; DOI=10.1371/journal.pgen.1004612;
RA Shin J.H., Chekanova J.A.;
RT "Arabidopsis RRP6L1 and RRP6L2 function in FLOWERING LOCUS C silencing via
RT regulation of antisense RNA synthesis.";
RL PLoS Genet. 10:E1004612-E1004612(2014).
CC -!- FUNCTION: Acts as an important epigenetic regulator through multiple
CC silencing mechanisms (PubMed:23555312, PubMed:24726328,
CC PubMed:24719467, PubMed:25211139). Involved in transcriptional gene
CC silencing (TGS). Plays a role for DNA methylation in the RNA-directed
CC DNA methylation (RdDM) pathway. Contributes to the methylation status
CC of the retrotransposon SN1. Required for DNA methylation only at a
CC subset of RdDM target loci (PubMed:24719467). Plays a regulatory role
CC in RdDM through retention of non-coding RNAs (ncRNAs) in normal cells.
CC Helps to retain Pol V-transcribed RNAs in chromatin to enable their
CC scaffold function and is required for genome-wide Pol IV-dependent
CC siRNA (24 nt siRNA) production that may involve retention of Pol IV
CC transcripts (PubMed:24726328). Involved in association with RRP6L2 in
CC the silencing of the solo LTR locus. Controls levels of ncRNAs from the
CC solo LTR locus. Seems to function independently of the RdDM pathway
CC (PubMed:23555312). Functions redundantly with RRP6L2 in the regulation
CC of FLC locus. Participates in the maintenance of trimethylated 'Lys-27'
CC (H3K27me3) at FLC locus via the regulation of antisense long non-coding
CC RNAs (lncRNAs) and the regulation of diverse antisense RNAs derived
CC from the FLC locus (PubMed:25211139). Seems not involved in the
CC exosomal RNA degradation (PubMed:24726328, PubMed:25211139). Can
CC complement the growth defect of a yeast mutant lacking RRP6 exonuclease
CC (PubMed:18285452). {ECO:0000269|PubMed:18285452,
CC ECO:0000269|PubMed:23555312, ECO:0000269|PubMed:24719467,
CC ECO:0000269|PubMed:24726328, ECO:0000269|PubMed:25211139}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:18285452}. Nucleus,
CC nucleoplasm {ECO:0000269|PubMed:18285452}. Note=Also detected in the
CC nucleolar vacuole. {ECO:0000269|PubMed:18285452}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=1;
CC Comment=A number of isoforms are produced. According to EST
CC sequences. {ECO:0000305};
CC Name=1;
CC IsoId=Q0WVE8-1; Sequence=Displayed;
CC -!- DISRUPTION PHENOTYPE: No visible phenotype under normal growth
CC conditions (PubMed:18285452, PubMed:25211139). The double mutants
CC rrp6l1 and rrp6l2 have a late flowering phenotype (PubMed:25211139).
CC {ECO:0000269|PubMed:18285452, ECO:0000269|PubMed:25211139}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAD25623.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=BAF01584.1; Type=Frameshift; Evidence={ECO:0000305};
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; EU240662; ABX52079.1; -; mRNA.
DR EMBL; AC005287; AAD25623.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002684; AEE33102.1; -; Genomic_DNA.
DR EMBL; AK226803; BAE98900.1; -; mRNA.
DR EMBL; AK229747; BAF01584.1; ALT_FRAME; mRNA.
DR PIR; C96586; C96586.
DR RefSeq; NP_175846.3; NM_104322.5. [Q0WVE8-1]
DR AlphaFoldDB; Q0WVE8; -.
DR SMR; Q0WVE8; -.
DR IntAct; Q0WVE8; 1.
DR STRING; 3702.AT1G54440.2; -.
DR iPTMnet; Q0WVE8; -.
DR PaxDb; Q0WVE8; -.
DR PRIDE; Q0WVE8; -.
DR EnsemblPlants; AT1G54440.1; AT1G54440.1; AT1G54440. [Q0WVE8-1]
DR GeneID; 841886; -.
DR Gramene; AT1G54440.1; AT1G54440.1; AT1G54440. [Q0WVE8-1]
DR KEGG; ath:AT1G54440; -.
DR Araport; AT1G54440; -.
DR eggNOG; KOG2206; Eukaryota.
DR PhylomeDB; Q0WVE8; -.
DR PRO; PR:Q0WVE8; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q0WVE8; baseline and differential.
DR Genevisible; Q0WVE8; AT.
DR GO; GO:0000176; C:nuclear exosome (RNase complex); IBA:GO_Central.
DR GO; GO:0005730; C:nucleolus; IDA:UniProtKB.
DR GO; GO:0005654; C:nucleoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0000175; F:3'-5'-exoribonuclease activity; IMP:UniProtKB.
DR GO; GO:0000166; F:nucleotide binding; IEA:InterPro.
DR GO; GO:0003727; F:single-stranded RNA binding; IBA:GO_Central.
DR GO; GO:0000467; P:exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA); IBA:GO_Central.
DR GO; GO:0080188; P:gene silencing by RNA-directed DNA methylation; IMP:UniProtKB.
DR GO; GO:0071044; P:histone mRNA catabolic process; IBA:GO_Central.
DR GO; GO:0071040; P:nuclear polyadenylation-dependent antisense transcript catabolic process; IBA:GO_Central.
DR GO; GO:0071039; P:nuclear polyadenylation-dependent CUT catabolic process; IBA:GO_Central.
DR GO; GO:0071035; P:nuclear polyadenylation-dependent rRNA catabolic process; IBA:GO_Central.
DR GO; GO:0071036; P:nuclear polyadenylation-dependent snoRNA catabolic process; IBA:GO_Central.
DR GO; GO:0071037; P:nuclear polyadenylation-dependent snRNA catabolic process; IBA:GO_Central.
DR GO; GO:0071038; P:nuclear polyadenylation-dependent tRNA catabolic process; IBA:GO_Central.
DR GO; GO:0071051; P:polyadenylation-dependent snoRNA 3'-end processing; IBA:GO_Central.
DR GO; GO:1902466; P:positive regulation of histone H3-K27 trimethylation; IMP:UniProtKB.
DR Gene3D; 1.10.150.80; -; 1.
DR Gene3D; 3.30.420.10; -; 1.
DR InterPro; IPR002562; 3'-5'_exonuclease_dom.
DR InterPro; IPR010997; HRDC-like_sf.
DR InterPro; IPR002121; HRDC_dom.
DR InterPro; IPR044876; HRDC_dom_sf.
DR InterPro; IPR012337; RNaseH-like_sf.
DR InterPro; IPR036397; RNaseH_sf.
DR InterPro; IPR045092; Rrp6-like.
DR PANTHER; PTHR12124; PTHR12124; 1.
DR Pfam; PF01612; DNA_pol_A_exo1; 1.
DR Pfam; PF00570; HRDC; 1.
DR SMART; SM00474; 35EXOc; 1.
DR SMART; SM00341; HRDC; 1.
DR SUPFAM; SSF47819; SSF47819; 1.
DR SUPFAM; SSF53098; SSF53098; 1.
DR PROSITE; PS50967; HRDC; 1.
PE 2: Evidence at transcript level;
KW Alternative splicing; Nucleus; Reference proteome;
KW RNA-mediated gene silencing.
FT CHAIN 1..637
FT /note="Protein RRP6-like 1"
FT /id="PRO_0000433630"
FT DOMAIN 118..283
FT /note="3'-5' exonuclease"
FT /evidence="ECO:0000255"
FT DOMAIN 334..414
FT /note="HRDC"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00328"
FT REGION 553..624
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 581..597
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 637 AA; 73483 MW; 782460E74329BF9E CRC64;
MRFDDPMDEF KRNRKMEEDS KKVIDVKVAE SDKGFAKFGK AEVPFHIPTL TKPQEEYKIL
VDNANNPFEH VLLEKSEDGL RFIHPLEELS VMDFVDRNLS EMRPVKPLPL EETPFKLVEE
VKDLEDLAAA LQSVEEFAVD LEHNQYRTFQ GLTCLMQIST RTEDYIVDIF KLWDHIGPYL
RELFKDPKKK KVIHGADRDI IWLQRDFGIY VCNLFDTGQA SRVLKLERNS LEFLLKHYCG
VAANKEYQKA DWRIRPLPDV MKRYAREDTH YLLYIYDVMR MELHTMAKED EQSDSPLVEV
YKRSYDVCMQ LYEKELWTRD SYLHVYGVQT GNLNAVQLSI VAGLCEWRDR IARADDESTG
YVLPNKTLFD IAKEMPIVVA QLRRLLKSKL PYLERNFDAV ISVIRRSMQN AAAFEPVVQS
LKDRRPETVV EMNIEPKIEK TDTGASASSL SLEKVCVDDS KKQSSGFGVL PLKRKLESDK
TVVEKNIEPK IEKTGTEASA SSLSSKKVCV DDSKKQSSGF GVLLSKRKFE SDNKVKEEVK
VSKSKPDKVI IVVDDDDDDD DDESYEQSTK AADALDRVSE TPSKGSPSLT QKPKTCNTEV
IVLDDDDDSE SREDEDMRRR SEKHRRFMNM KRGFLNI
