RENT3_ARATH
ID RENT3_ARATH Reviewed; 482 AA.
AC Q9FVW4; B3H5N7; Q9FX10;
DT 03-APR-2013, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2001, sequence version 1.
DT 03-AUG-2022, entry version 138.
DE RecName: Full=Regulator of nonsense transcripts UPF3 {ECO:0000305};
DE AltName: Full=Nonsense mRNA reducing factor UPF3 {ECO:0000305};
DE AltName: Full=Up-frameshift suppressor 3 homolog {ECO:0000305};
DE Short=AtUpf3 {ECO:0000303|PubMed:16098107};
GN Name=UPF3 {ECO:0000303|PubMed:16098107};
GN OrderedLocusNames=At1g33980 {ECO:0000312|Araport:AT1G33980};
GN ORFNames=F12G12.20 {ECO:0000312|EMBL:AAG12537.1},
GN T15K4.3 {ECO:0000312|EMBL:AAG12847.1};
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 [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 [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;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [4]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=16098107; DOI=10.1111/j.1365-313x.2005.02473.x;
RA Hori K., Watanabe Y.;
RT "UPF3 suppresses aberrant spliced mRNA in Arabidopsis.";
RL Plant J. 43:530-540(2005).
RN [5]
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 [6]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19376835; DOI=10.1104/pp.109.138677;
RA Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A.,
RA Grossmann J., Gruissem W., Baginsky S.;
RT "Large-scale Arabidopsis phosphoproteome profiling reveals novel
RT chloroplast kinase substrates and phosphorylation networks.";
RL Plant Physiol. 150:889-903(2009).
RN [7]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=19181858; DOI=10.1073/pnas.0808902106;
RA Kurihara Y., Matsui A., Hanada K., Kawashima M., Ishida J., Morosawa T.,
RA Tanaka M., Kaminuma E., Mochizuki Y., Matsushima A., Toyoda T.,
RA Shinozaki K., Seki M.;
RT "Genome-wide suppression of aberrant mRNA-like noncoding RNAs by NMD in
RT Arabidopsis.";
RL Proc. Natl. Acad. Sci. U.S.A. 106:2453-2458(2009).
RN [8]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. Columbia;
RX PubMed=19863731; DOI=10.1111/j.1469-8137.2009.03065.x;
RA Palusa S.G., Reddy A.S.;
RT "Extensive coupling of alternative splicing of pre-mRNAs of serine/arginine
RT (SR) genes with nonsense-mediated decay.";
RL New Phytol. 185:83-89(2010).
RN [9]
RP FUNCTION, DISRUPTION PHENOTYPE, AND DOWN-REGULATION BY PSEUDOMONAS
RP SYRINGAE.
RC STRAIN=cv. Columbia;
RX PubMed=22025558; DOI=10.1093/pcp/pcr144;
RA Jeong H.-J., Kim Y.J., Kim S.H., Kim Y.-H., Lee I.-J., Kim Y.K., Shin J.S.;
RT "Nonsense-mediated mRNA decay factors, UPF1 and UPF3, contribute to plant
RT defense.";
RL Plant Cell Physiol. 52:2147-2156(2011).
RN [10]
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).
RN [11]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. Columbia;
RX PubMed=22127866; DOI=10.1093/nar/gkr932;
RA Kalyna M., Simpson C.G., Syed N.H., Lewandowska D., Marquez Y., Kusenda B.,
RA Marshall J., Fuller J., Cardle L., McNicol J., Dinh H.Q., Barta A.,
RA Brown J.W.S.;
RT "Alternative splicing and nonsense-mediated decay modulate expression of
RT important regulatory genes in Arabidopsis.";
RL Nucleic Acids Res. 40:2454-2469(2012).
RN [12]
RP INTERACTION WITH CPL1/FRY2, AND SUBCELLULAR LOCATION.
RX PubMed=26887918; DOI=10.1105/tpc.15.00771;
RA Cui P., Chen T., Qin T., Ding F., Wang Z., Chen H., Xiong L.;
RT "The RNA polymerase II C-terminal domain phosphatase-like protein
RT FIERY2/CPL1 interacts with eIF4AIII and is essential for nonsense-mediated
RT mrna decay in Arabidopsis.";
RL Plant Cell 28:770-785(2016).
CC -!- FUNCTION: Recruits UPF2 at the cytoplasmic side of the nuclear envelope
CC and the subsequent formation of an UPF1-UPF2-UPF3 surveillance complex
CC (including UPF1 bound to release factors at the stalled ribosome) is
CC believed to activate NMD. Binds spliced mRNA upstream of exon-exon
CC junctions (By similarity). Involved in nonsense-mediated decay (NMD) of
CC mRNAs containing premature stop codons (premature termination codon
CC PTC) by associating with the nuclear exon junction complex (EJC) and
CC serving as link between the EJC core and NMD machinery. Eliminates the
CC production of nonsense-containing RNAs (ncRNAs). Required for plant
CC development and adaptation to environmental stresses, including plant
CC defense and response to wounding. {ECO:0000250,
CC ECO:0000269|PubMed:16098107, ECO:0000269|PubMed:19181858,
CC ECO:0000269|PubMed:19863731, ECO:0000269|PubMed:22025558,
CC ECO:0000269|PubMed:22127866, 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 CPL1/FRY2 (PubMed:26887918). {ECO:0000250,
CC ECO:0000269|PubMed:26887918}.
CC -!- SUBCELLULAR LOCATION: Nucleus, nucleolus {ECO:0000269|PubMed:19602621}.
CC Nucleus {ECO:0000269|PubMed:26887918}. Cytoplasm {ECO:0000250}.
CC Note=Shuttling between the nucleus and the cytoplasm. {ECO:0000250}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q9FVW4-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q9FVW4-2; Sequence=VSP_046161;
CC -!- INDUCTION: Down-regulated upon Pseudomonas syringae pv. tomato strain
CC DC3000 infection. {ECO:0000269|PubMed:22025558}.
CC -!- DISRUPTION PHENOTYPE: Seedling lethal. Reduced ability to degrade mRNAs
CC with premature termination codons (PTC). Increased expression of not
CC only protein-coding transcripts but also many mRNA-like nonprotein-
CC coding RNAs (mlncRNAs), including natural antisense transcript RNAs
CC (nat-RNAs). Dwarf with curly leaves and late flowering. Photoperiod-
CC dependent altered development and stress responses; in long days (16
CC hours light), altered organ morphologies (e.g. narrow and epinastic
CC leaves with wide petiole, small rosette size, long seeds, some abnormal
CC flowers and stunted stem growth), disturbed homeostasis of wounding-
CC induced jasmonic acid and pathogen-elicited salicylic acid. Increased
CC resistance to Pseudomonas syringae pv. tomato strain DC3000.
CC {ECO:0000269|PubMed:16098107, ECO:0000269|PubMed:19181858,
CC ECO:0000269|PubMed:19863731, ECO:0000269|PubMed:22025558,
CC ECO:0000269|PubMed:22127866, ECO:0000269|PubMed:22353561}.
CC -!- SIMILARITY: Belongs to the RENT3 family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAG12537.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AC015446; AAG12537.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AC079286; AAG12847.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE31653.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE31654.1; -; Genomic_DNA.
DR EMBL; AY128383; AAM91586.1; -; mRNA.
DR EMBL; BT000112; AAN15431.1; -; mRNA.
DR PIR; E86463; E86463.
DR RefSeq; NP_001117406.1; NM_001123934.1. [Q9FVW4-2]
DR RefSeq; NP_174660.2; NM_103120.4. [Q9FVW4-1]
DR AlphaFoldDB; Q9FVW4; -.
DR SMR; Q9FVW4; -.
DR STRING; 3702.AT1G33980.2; -.
DR iPTMnet; Q9FVW4; -.
DR PaxDb; Q9FVW4; -.
DR PRIDE; Q9FVW4; -.
DR ProteomicsDB; 225963; -. [Q9FVW4-1]
DR EnsemblPlants; AT1G33980.1; AT1G33980.1; AT1G33980. [Q9FVW4-1]
DR EnsemblPlants; AT1G33980.2; AT1G33980.2; AT1G33980. [Q9FVW4-2]
DR GeneID; 840295; -.
DR Gramene; AT1G33980.1; AT1G33980.1; AT1G33980. [Q9FVW4-1]
DR Gramene; AT1G33980.2; AT1G33980.2; AT1G33980. [Q9FVW4-2]
DR KEGG; ath:AT1G33980; -.
DR Araport; AT1G33980; -.
DR TAIR; locus:2009026; AT1G33980.
DR eggNOG; KOG1295; Eukaryota.
DR HOGENOM; CLU_023010_1_0_1; -.
DR InParanoid; Q9FVW4; -.
DR OMA; ERAIYQP; -.
DR OrthoDB; 802385at2759; -.
DR PhylomeDB; Q9FVW4; -.
DR PRO; PR:Q9FVW4; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q9FVW4; baseline and differential.
DR Genevisible; Q9FVW4; AT.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005730; C:nucleolus; IDA:UniProtKB.
DR GO; GO:0005634; C:nucleus; HDA:TAIR.
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:0051028; P:mRNA transport; IEA:UniProtKB-KW.
DR GO; GO:0000184; P:nuclear-transcribed mRNA catabolic process, nonsense-mediated decay; IMP:UniProtKB.
DR GO; GO:0045727; P:positive regulation of translation; IBA:GO_Central.
DR GO; GO:0009611; P:response to wounding; IMP:UniProtKB.
DR GO; GO:0009863; P:salicylic acid mediated signaling pathway; IMP:UniProtKB.
DR Gene3D; 3.30.70.330; -; 1.
DR InterPro; IPR012677; Nucleotide-bd_a/b_plait_sf.
DR InterPro; IPR035979; RBD_domain_sf.
DR InterPro; IPR039722; Upf3.
DR InterPro; IPR005120; UPF3_dom.
DR PANTHER; PTHR13112; PTHR13112; 1.
DR Pfam; PF03467; Smg4_UPF3; 1.
DR SUPFAM; SSF54928; SSF54928; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; Cytoplasm; mRNA transport;
KW Nonsense-mediated mRNA decay; Nucleus; Plant defense; Reference proteome;
KW RNA-binding; Transport.
FT CHAIN 1..482
FT /note="Regulator of nonsense transcripts UPF3"
FT /id="PRO_0000421875"
FT REGION 9..219
FT /note="Necessary for interaction with UPF2"
FT REGION 9..14
FT /note="Binds to UPF2"
FT /evidence="ECO:0000250"
FT REGION 53..482
FT /note="Sufficient for association with EJC core"
FT /evidence="ECO:0000250"
FT REGION 173..482
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 198..218
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 219..243
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 268..283
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 288..309
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 322..340
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 364..391
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 397..432
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT VAR_SEQ 47
FT /note="S -> RLG (in isoform 2)"
FT /evidence="ECO:0000305"
FT /id="VSP_046161"
SQ SEQUENCE 482 AA; 53804 MW; 230CAC206E160540 CRC64;
MKEPLQKKKV VVRHLPPSLS QSDLLSQIDP RFADRYNWVS FRPGKSSYKN QKYSRAYVSF
KAPEDVYEFA AFFNGHVFVN EKGAQFKAIV EYAPSQRVPK PSDKKDPREG SISKDPDYLE
FLKVIAQPVE NLPSAEIQLE RREAEQSGAS KAAPIVTPLM EFIRQKRATV MGPQGLSDIR
RGGRRTRVVS ANKPSPRPSK RNSEKKKYVE KESSKNVPRK TTADVSSSKP DYRQSNSSGK
ELPGNETAAI IDSSPPGIAL TMDSGKKKIL LLRSKDRDNP DNPPPQPEQH IDTNLSRNST
DSRQNQKSDV GGRLIKGILL RNDSRPSQSS TFVQSEQRVE PSEAENYKRP SRPANTRAGK
DYHTSGTISE KQERRTRNKD RPDRVMWAPR RDGSEDQPLS SAGNNGEVKD RMFSQRSGEV
VNSSGGHTLE NGSARHSSRR VGGRNRKEEV VIGEGKTSRR GSGGGPSSHE KQMWIQKPSS
GT
