RP6L2_ARATH
ID RP6L2_ARATH Reviewed; 870 AA.
AC A9LLI7; Q9FFL2;
DT 16-SEP-2015, integrated into UniProtKB/Swiss-Prot.
DT 05-FEB-2008, sequence version 1.
DT 03-AUG-2022, entry version 104.
DE RecName: Full=Protein RRP6-like 2 {ECO:0000303|PubMed:18285452};
DE Short=AtRRP6L2 {ECO:0000303|PubMed:18285452};
GN Name=RRP6L2 {ECO:0000303|PubMed:18285452};
GN OrderedLocusNames=At5g35910 {ECO:0000312|Araport:AT5G35910};
GN ORFNames=MIK22.22 {ECO:0000312|EMBL:BAB09932.1};
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=9330910; DOI=10.1093/dnares/4.3.215;
RA Sato S., Kotani H., Nakamura Y., Kaneko T., Asamizu E., Fukami M.,
RA Miyajima N., Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. I. Sequence
RT features of the 1.6 Mb regions covered by twenty physically assigned P1
RT clones.";
RL DNA Res. 4:215-230(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RA Kaneko T., Katoh T., Asamizu E., Sato S., Nakamura Y., Kotani H.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. XI.";
RL Submitted (APR-1999) to the EMBL/GenBank/DDBJ databases.
RN [4]
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 [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, 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:25211139). Involved in
CC association with RRP6L1 in the silencing of the solo LTR locus.
CC Controls levels of non-coding RNAs (ncRNAs) from the solo LTR locus.
CC Seems to function independently of the RNA-mediated gene silencing
CC (RdDM) pathway (PubMed:23555312). Functions redundantly with RRP6L1 in
CC the regulation of FLC locus. Participates in the maintenance of
CC trimethylated 'Lys-27' (H3K27me3) at FLC locus via the regulation of
CC antisense long non-coding RNAs (lncRNAs) and the regulation of diverse
CC antisense RNAs derived from the FLC locus. Seems not involved in the
CC exosomal RNA degradation (PubMed:25211139). May be involved in poly(A)-
CC mediated RNA degradation (PubMed:18285452).
CC {ECO:0000269|PubMed:18285452, ECO:0000269|PubMed:23555312,
CC ECO:0000269|PubMed:25211139}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:18285452}. Nucleus,
CC nucleolus {ECO:0000269|PubMed:18285452}. Cytoplasm
CC {ECO:0000269|PubMed:18285452}. Note=Localizes predominantly in the
CC nucleus. {ECO:0000269|PubMed:18285452}.
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=BAB09932.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; EU240663; ABX52080.1; -; mRNA.
DR EMBL; AB005236; BAB09932.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AB025602; BAB09932.1; JOINED; Genomic_DNA.
DR EMBL; CP002688; AED94025.1; -; Genomic_DNA.
DR RefSeq; NP_198440.2; NM_122982.4.
DR AlphaFoldDB; A9LLI7; -.
DR SMR; A9LLI7; -.
DR STRING; 3702.AT5G35910.1; -.
DR iPTMnet; A9LLI7; -.
DR PaxDb; A9LLI7; -.
DR PRIDE; A9LLI7; -.
DR ProteomicsDB; 227971; -.
DR EnsemblPlants; AT5G35910.1; AT5G35910.1; AT5G35910.
DR GeneID; 833577; -.
DR Gramene; AT5G35910.1; AT5G35910.1; AT5G35910.
DR KEGG; ath:AT5G35910; -.
DR Araport; AT5G35910; -.
DR TAIR; locus:2165189; AT5G35910.
DR eggNOG; KOG2206; Eukaryota.
DR HOGENOM; CLU_010129_4_1_1; -.
DR InParanoid; A9LLI7; -.
DR OMA; ANCDAFE; -.
DR OrthoDB; 677201at2759; -.
DR PhylomeDB; A9LLI7; -.
DR PRO; PR:A9LLI7; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; A9LLI7; baseline and differential.
DR Genevisible; A9LLI7; AT.
DR GO; GO:0005737; C:cytoplasm; IDA:UniProtKB.
DR GO; GO:0000176; C:nuclear exosome (RNase complex); IBA:GO_Central.
DR GO; GO:0005730; C:nucleolus; IDA:UniProtKB.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0000175; F:3'-5'-exoribonuclease activity; IBA:GO_Central.
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:0043633; P:polyadenylation-dependent RNA catabolic process; IMP:UniProtKB.
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 GO; GO:0006364; P:rRNA processing; IMP:TAIR.
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 Cytoplasm; Exonuclease; Hydrolase; Nuclease; Nucleus; Reference proteome;
KW RNA-mediated gene silencing.
FT CHAIN 1..870
FT /note="Protein RRP6-like 2"
FT /id="PRO_0000433631"
FT DOMAIN 263..428
FT /note="3'-5' exonuclease"
FT /evidence="ECO:0000255"
FT DOMAIN 479..559
FT /note="HRDC"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00328"
FT REGION 583..605
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 649..668
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 688..775
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 821..870
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 688..703
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 722..737
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 739..753
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 760..775
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 821..835
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 870 AA; 97889 MW; 0283C0DF1EC945C4 CRC64;
MSDGNMDVDE SPVSWKVKSL EKLIDGSSFS STLSRLSSSS RLIPTSRDFH FYYNFDEFKR
PIDEITGTSQ STLATIGDSE QVWGKSMKFP GDVDDVYAED WLCNVNDELI ERFDVSVDEF
QRIRKKEKEI GRSVVADDGD DGFQMVYGKK KKPVGNVVTG SAAVNGGGSV IDVKMAERDK
NSSGKAKVPF HVPTIKKPQE EYNILVNNAN LPFEHVWLER SEDDLRAMHP LEKFSVLDFV
DKDVNEMEPV KPLPLEQTPF KFVQEVKDLK ELVAKLRSVE EFAVDLEHNQ YRSFQGLTCL
MQISTRTEDY IVDTFKLRIH IGPYLREIFK DPKKKKVMHG ADRDIIWLQR DFGIYVCNLF
DTGQASRVLN LERNSLEFLL QHFCGVTANK EYQNADWRIR PLPEEMTRYA REDTHYLLYI
YDLIKLELQR MAKDDAHTDS PLLEVYKRSY DVCTQLYEKE LLTENSYLHV YGLQAAGFNA
AQLAIVAGLC EWRDFIARAE DESTGYVLPN KVLLEIAKEM PDSVGKLRRM LKSKHPYIER
NVDSVVSVIR QSMQHYAAFE SAALSLKDVS PGNVMDKNIE PISEKKDLHT GDVASPSLKE
NSSQLESTRD LIMGAANTNE GRGLGSGLFG SAKVSAAVRI SKKPSSGLGA LLGNAASKKK
SRTDEKVKED VKLEQIRSSV NLSFHSFTEK VPDSKSTSET SPKVYGKPEE MSSTMPASVS
KEDGVKELKD DSEEASEIVG TSGRVSESKV SSSEMGDIIL LENGDEKKVD AEDEPMSLSE
LSTNFQKCFK SMNKSKKAQK QTEFLNIEPF DYEAARKEVK FGEGHKGRQG KREAAAGQKK
GSTQEQSEFG QGKRRQAFPA SGNRSMSFKN
