RENT2_ARATH
ID RENT2_ARATH Reviewed; 1181 AA.
AC F4IUX6; O80955;
DT 03-APR-2013, integrated into UniProtKB/Swiss-Prot.
DT 28-JUN-2011, sequence version 1.
DT 25-MAY-2022, entry version 64.
DE RecName: Full=Regulator of nonsense transcripts UPF2;
DE AltName: Full=Nonsense mRNA reducing factor UPF2;
DE AltName: Full=Up-frameshift suppressor 2 homolog;
DE Short=AtUpf2;
GN Name=UPF2; OrderedLocusNames=At2g39260; ORFNames=T16B24.10;
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=10617197; DOI=10.1038/45471;
RA Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D.,
RA Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V.,
RA Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L., Moffat K.S.,
RA Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L., Tallon L.J.,
RA Gill J.E., Adams M.D., Carrera A.J., Creasy T.H., Goodman H.M.,
RA Somerville C.R., Copenhaver G.P., Preuss D., Nierman W.C., White O.,
RA Eisen J.A., Salzberg S.L., Fraser C.M., Venter J.C.;
RT "Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.";
RL Nature 402:761-768(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].
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 [4]
RP SUBCELLULAR LOCATION.
RX PubMed=19602621; DOI=10.1105/tpc.109.067736;
RA Kim S.H., Koroleva O.A., Lewandowska D., Pendle A.F., Clark G.P.,
RA Simpson C.G., Shaw P.J., Brown J.W.S.;
RT "Aberrant mRNA transcripts and the nonsense-mediated decay proteins UPF2
RT and UPF3 are enriched in the Arabidopsis nucleolus.";
RL Plant Cell 21:2045-2057(2009).
RN [5]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. Columbia;
RX PubMed=22353561; DOI=10.1111/j.1744-7909.2012.01093.x;
RA Shi C., Baldwin I.T., Wu J.;
RT "Arabidopsis plants having defects in nonsense-mediated mRNA decay factors
RT UPF1, UPF2, and UPF3 show photoperiod-dependent phenotypes in development
RT and stress responses.";
RL J. Integr. Plant Biol. 54:99-114(2012).
CC -!- FUNCTION: Recruited by UPF3 associated with the EJC core at the
CC cytoplasmic side of the nuclear envelope and the subsequent formation
CC of an UPF1-UPF2-UPF3 surveillance complex (including UPF1 bound to
CC release factors at the stalled ribosome) is believed to activate NMD.
CC In cooperation with UPF3 stimulates both ATPase and RNA helicase
CC activities of UPF1. Binds spliced mRNA (By similarity). Involved in
CC nonsense-mediated decay (NMD) of mRNAs containing premature stop codons
CC by associating with the nuclear exon junction complex (EJC). Required
CC for plant development and adaptation to environmental stresses,
CC including plant defense and response to wounding. {ECO:0000250,
CC ECO:0000269|PubMed:22353561}.
CC -!- SUBUNIT: Found in a post-splicing messenger ribonucleoprotein (mRNP)
CC complex. Associates with the exon junction complex (EJC). Interacts
CC with UPF1 and UPF3 (By similarity). {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Nucleus, nucleolus {ECO:0000269|PubMed:19602621}.
CC Cytoplasm {ECO:0000269|PubMed:19602621}. Cytoplasm, perinuclear region
CC {ECO:0000250}.
CC -!- DISRUPTION PHENOTYPE: Seedling lethal. Accumulation of mRNAs with
CC premature termination codons (PTC). Photoperiod-dependent altered
CC development and stress responses; in long days (16 hours light),
CC altered organ morphologies (e.g. epinastic leaves, small rosette size,
CC long seeds, some abnormal flowers and stunted stem growth), disturbed
CC homeostasis of wounding-induced jasmonic acid and pathogen-elicited
CC salicylic acid. Increased resistance to Pseudomonas syringae pv. tomato
CC strain DC3000. {ECO:0000269|PubMed:22353561}.
CC -!- SIMILARITY: Belongs to the RENT2 family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAC28982.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=AK227294; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; AC004697; AAC28982.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002685; AEC09651.1; -; Genomic_DNA.
DR EMBL; AK227294; -; NOT_ANNOTATED_CDS; mRNA.
DR PIR; T02576; T02576.
DR RefSeq; NP_181459.4; NM_129484.5.
DR AlphaFoldDB; F4IUX6; -.
DR SMR; F4IUX6; -.
DR STRING; 3702.AT2G39260.1; -.
DR iPTMnet; F4IUX6; -.
DR PaxDb; F4IUX6; -.
DR PRIDE; F4IUX6; -.
DR ProteomicsDB; 236871; -.
DR EnsemblPlants; AT2G39260.1; AT2G39260.1; AT2G39260.
DR GeneID; 818511; -.
DR Gramene; AT2G39260.1; AT2G39260.1; AT2G39260.
DR KEGG; ath:AT2G39260; -.
DR Araport; AT2G39260; -.
DR TAIR; locus:2056038; AT2G39260.
DR eggNOG; KOG2051; Eukaryota.
DR HOGENOM; CLU_002633_2_0_1; -.
DR InParanoid; F4IUX6; -.
DR OMA; DFQHHQI; -.
DR OrthoDB; 653534at2759; -.
DR PRO; PR:F4IUX6; -.
DR Proteomes; UP000006548; Chromosome 2.
DR ExpressionAtlas; F4IUX6; baseline and differential.
DR Genevisible; F4IUX6; AT.
DR GO; GO:0005737; C:cytoplasm; IDA:UniProtKB.
DR GO; GO:0035145; C:exon-exon junction complex; IBA:GO_Central.
DR GO; GO:0005730; C:nucleolus; IDA:UniProtKB.
DR GO; GO:0048471; C:perinuclear region of cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005844; C:polysome; IBA:GO_Central.
DR GO; GO:0003729; F:mRNA binding; HDA:TAIR.
DR GO; GO:0042742; P:defense response to bacterium; IMP:UniProtKB.
DR GO; GO:0009867; P:jasmonic acid mediated signaling pathway; IMP:UniProtKB.
DR GO; GO:0048571; P:long-day photoperiodism; IMP:UniProtKB.
DR GO; GO:0000184; P:nuclear-transcribed mRNA catabolic process, nonsense-mediated decay; IMP:UniProtKB.
DR GO; GO:0009611; P:response to wounding; IMP:UniProtKB.
DR GO; GO:0009863; P:salicylic acid mediated signaling pathway; IMP:UniProtKB.
DR InterPro; IPR016024; ARM-type_fold.
DR InterPro; IPR003890; MIF4G-like_typ-3.
DR InterPro; IPR039762; Nmd2/UPF2.
DR InterPro; IPR007193; Upf2/Nmd2_C.
DR PANTHER; PTHR12839; PTHR12839; 1.
DR Pfam; PF02854; MIF4G; 3.
DR Pfam; PF04050; Upf2; 1.
DR SMART; SM00543; MIF4G; 3.
DR SUPFAM; SSF48371; SSF48371; 3.
PE 2: Evidence at transcript level;
KW Coiled coil; Cytoplasm; Nonsense-mediated mRNA decay; Nucleus;
KW Plant defense; Reference proteome; Repeat; RNA-binding.
FT CHAIN 1..1181
FT /note="Regulator of nonsense transcripts UPF2"
FT /id="PRO_0000421874"
FT DOMAIN 61..264
FT /note="MIF4G 1"
FT DOMAIN 469..655
FT /note="MIF4G 2"
FT DOMAIN 672..871
FT /note="MIF4G 3"
FT REGION 309..348
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 375..459
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 735..755
FT /note="Binds to UPF3"
FT /evidence="ECO:0000250"
FT REGION 893..991
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 981..1181
FT /note="Sufficient for interaction with UPF1 C-terminus"
FT /evidence="ECO:0000250"
FT REGION 999..1102
FT /note="Necessary for interaction with UPF1"
FT /evidence="ECO:0000250"
FT REGION 999..1023
FT /note="Interaction with UPF1"
FT /evidence="ECO:0000250"
FT REGION 1066..1111
FT /note="Interaction with UPF1"
FT /evidence="ECO:0000250"
FT REGION 1129..1181
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 6..41
FT /evidence="ECO:0000255"
FT COILED 260..309
FT /evidence="ECO:0000255"
FT COILED 425..451
FT /evidence="ECO:0000255"
FT COILED 539..559
FT /evidence="ECO:0000255"
FT COILED 1000..1021
FT /evidence="ECO:0000255"
FT COMPBIAS 378..392
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 393..417
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 418..459
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 893..912
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 913..928
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 929..943
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 955..972
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1135..1157
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 1181 AA; 133962 MW; 17C1964D4C402B65 CRC64;
MDHPEDESHS EKQDDEEALA RLEEIKKSIE AKLTLRQNNL NPERPDSAYL RTLDSSIKRN
TAVIKKLKQI NEEQREGLMD DLRGVNLSKF VSEAVTAICE AKLKSSDIQA AVQICSLLHQ
RYKEFSASLT QGLLKVFFPG KSAEDLEADK NSKAMKKRST LKLLLELYYV GVIEDSNIFI
NIIKDLTSVE QLKDRDTTQT NLTLLTSFAR QGRIFLGLPI SGQDEDFFKG LDVTADQKKS
FKKAFNTYYD ALADLLQSEH KLLLQMEKEN AKLVNAKGEL SEDSASSYEK LRKSYDHLYR
NISSLAEALD MQPPVMPEDG TTRLTAGDEA SPSGTVKDTS VPEPIWDDED TKTFYECLPD
LRAFVPAVLL GEAEPKSNEQ SAKAKEKLSE SSSEVVENQQ TTEDTTEVSA DSASMDDRSN
AEQPKEKEEV EKEKAKDTKK EKGKEKDSEK KMEHEKEKGK SLDVANFERL LQRLPGCVSR
DLIDQLTVEY CYLNSKTNRK KLVKALFNVP RTSLELLAYY SRMVATLASC MKDIPSMLVQ
MLEDEFNSLV HKKDQMNIET KIRNIRFIGE LCKFKIVPAG LVFSCLKACL DEFTHHNIDV
ACNLLETCGR FLYRSPETTL RMTNMLDILM RLKNVKNLDP RQSTLVENAY YLCKPPERSA
RISKVRPPLH QYVRKLLFSD LDKDSIANVL KQLRKLPWSE CEQYILKCFM KVHKGKYGQI
HLIASLTSGL SRHHDEFVVA VVDEVLEEIR VGLELNEYGA QQKRLAHMRF LGELYNYEHV
DSSVIFETLY LTLLYGHDTS EQEVLDPPED FFRVRMVIIL LETCGHYFDR GSSKKRLDQF
LIHFQRYILS KGHLPLDIEF DLQDLFANLR PNMTRYSTID EVNAAILQLE EREHASSGDK
VSIERHSDTK PSNKSSSDVI SSNGKSTAKD IRENGEAHGE ESDSDSGSGS VVRDGQNEEL
DDGNHERGSE SGDGDDYDDG DGPGSDDDKF RVRQKVVTVD LEEQADFDQE LKALLQESME
QRKLELRGRP ALNMTIPMSV FEGSGKDHHH FGRVVGENGE EVLDEENGEQ REVQVKVLVK
RGNKQQTRQM LIPSDCALVQ STKQKEAAEL EEKQDIKRLV LEYNERDEEE ANGLGTQILN
WTSGGSRGST RTGEGSGKSG GSRHRFYYHQ GGGGSYHARR K
