RENT1_ARATH
ID RENT1_ARATH Reviewed; 1254 AA.
AC Q9FJR0; Q8S3K7;
DT 18-OCT-2001, integrated into UniProtKB/Swiss-Prot.
DT 21-FEB-2006, sequence version 2.
DT 03-AUG-2022, entry version 136.
DE RecName: Full=Regulator of nonsense transcripts 1 homolog;
DE EC=3.6.4.12 {ECO:0000250|UniProtKB:Q92900};
DE EC=3.6.4.13 {ECO:0000250|UniProtKB:Q92900};
DE AltName: Full=ATP-dependent helicase UPF1;
GN Name=UPF1; Synonyms=LBA1; OrderedLocusNames=At5g47010; ORFNames=MQD22.15;
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=9734815; DOI=10.1093/dnares/5.3.203;
RA Kotani H., Nakamura Y., Sato S., Asamizu E., Kaneko T., Miyajima N.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. VI. Sequence
RT features of the regions of 1,367,185 bp covered by 19 physically assigned
RT P1 and TAC clones.";
RL DNA Res. 5:203-216(1998).
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 [MRNA] OF 12-1254.
RC STRAIN=cv. Columbia;
RA Johzuka Y., Mulligan M.R.;
RT "Cloning of the Upf1 gene in Arabidopsis.";
RL Submitted (FEB-2002) 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.
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 [6]
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 [7]
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 [8]
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 [9]
RP GENE FAMILY.
RX PubMed=24265739; DOI=10.1371/journal.pone.0078982;
RA Xu R., Zhang S., Huang J., Zheng C.;
RT "Genome-wide comparative in silico analysis of the RNA helicase gene family
RT in Zea mays and Glycine max: a comparison with Arabidopsis and Oryza
RT sativa.";
RL PLoS ONE 8:E78982-E78982(2013).
RN [10]
RP FUNCTION, MUTAGENESIS OF ARG-852, SUBCELLULAR LOCATION, DOMAINS, AND
RP PHOSPHORYLATION.
RX PubMed=22974464; DOI=10.1111/tpj.12015;
RA Merai Z., Benkovics A.H., Nyiko T., Debreczeny M., Hiripi L., Kerenyi Z.,
RA Kondorosi E., Silhavy D.;
RT "The late steps of plant nonsense-mediated mRNA decay.";
RL Plant J. 73:50-62(2013).
CC -!- FUNCTION: Involved in nonsense-mediated decay (NMD) of mRNAs containing
CC premature stop codons (premature termination codon PTC) by associating
CC with the nuclear exon junction complex (EJC) and serving as link
CC between the EJC core and NMD machinery. Eliminates the production of
CC nonsense-containing RNAs (ncRNAs). Required for plant development and
CC adaptation to environmental stresses, including plant defense and
CC response to wounding. {ECO:0000269|PubMed:19181858,
CC ECO:0000269|PubMed:22025558, ECO:0000269|PubMed:22127866,
CC ECO:0000269|PubMed:22353561, ECO:0000269|PubMed:22974464}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + H2O = ADP + H(+) + phosphate; Xref=Rhea:RHEA:13065,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:456216; EC=3.6.4.12;
CC Evidence={ECO:0000250|UniProtKB:Q92900};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:13066;
CC Evidence={ECO:0000250|UniProtKB:Q92900};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + H2O = ADP + H(+) + phosphate; Xref=Rhea:RHEA:13065,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:456216; EC=3.6.4.13;
CC Evidence={ECO:0000250|UniProtKB:Q92900};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:13066;
CC Evidence={ECO:0000250|UniProtKB:Q92900};
CC -!- SUBCELLULAR LOCATION: Cytoplasm. Cytoplasm, P-body. Note=Remobilize
CC from the cytoplasm into processing bodies by SMG7.
CC -!- INDUCTION: Down-regulated upon Pseudomonas syringae pv. tomato strain
CC DC3000 infection. {ECO:0000269|PubMed:22025558}.
CC -!- DOMAIN: The helicase ATP-binding domain is implicated in early steps of
CC nonsense-mediated decay (NMD). {ECO:0000269|PubMed:22974464}.
CC -!- PTM: Highly phosphorylated in S/TQ-enriched N-terminal and C-terminal
CC regions; required for formation of mRNA surveillance complexes.
CC {ECO:0000269|PubMed:22974464}.
CC -!- DISRUPTION PHENOTYPE: Seedling lethal. Increased expression of not only
CC protein-coding transcripts but also many mRNA-like nonprotein-coding
CC RNAs (mlncRNAs), including natural antisense transcript RNAs (nat-
CC 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:19181858, ECO:0000269|PubMed:22025558,
CC ECO:0000269|PubMed:22127866, ECO:0000269|PubMed:22353561}.
CC -!- SIMILARITY: Belongs to the DNA2/NAM7 helicase family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAB10240.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AB013394; BAB10240.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002688; AED95457.1; -; Genomic_DNA.
DR EMBL; AF484122; AAL92018.1; -; mRNA.
DR RefSeq; NP_199512.2; NM_124072.3.
DR AlphaFoldDB; Q9FJR0; -.
DR SMR; Q9FJR0; -.
DR BioGRID; 19995; 1.
DR STRING; 3702.AT5G47010.1; -.
DR iPTMnet; Q9FJR0; -.
DR PaxDb; Q9FJR0; -.
DR PRIDE; Q9FJR0; -.
DR ProteomicsDB; 236258; -.
DR EnsemblPlants; AT5G47010.1; AT5G47010.1; AT5G47010.
DR GeneID; 834747; -.
DR Gramene; AT5G47010.1; AT5G47010.1; AT5G47010.
DR KEGG; ath:AT5G47010; -.
DR Araport; AT5G47010; -.
DR TAIR; locus:2171007; AT5G47010.
DR eggNOG; KOG1802; Eukaryota.
DR HOGENOM; CLU_001666_4_3_1; -.
DR InParanoid; Q9FJR0; -.
DR OMA; HHDSIGY; -.
DR OrthoDB; 62494at2759; -.
DR PhylomeDB; Q9FJR0; -.
DR PRO; PR:Q9FJR0; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q9FJR0; baseline and differential.
DR Genevisible; Q9FJR0; AT.
DR GO; GO:0005737; C:cytoplasm; IDA:UniProtKB.
DR GO; GO:0005829; C:cytosol; IDA:TAIR.
DR GO; GO:0000932; C:P-body; IDA:TAIR.
DR GO; GO:0009506; C:plasmodesma; HDA:TAIR.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016887; F:ATP hydrolysis activity; IEA:RHEA.
DR GO; GO:0003677; F:DNA binding; IEA:InterPro.
DR GO; GO:0003729; F:mRNA binding; HDA:TAIR.
DR GO; GO:0003723; F:RNA binding; IBA:GO_Central.
DR GO; GO:0003724; F:RNA helicase activity; IBA:GO_Central.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
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:0008380; P:RNA splicing; IMP:TAIR.
DR GO; GO:0009863; P:salicylic acid mediated signaling pathway; IMP:UniProtKB.
DR GO; GO:0010182; P:sugar mediated signaling pathway; IMP:TAIR.
DR GO; GO:0006412; P:translation; IMP:TAIR.
DR CDD; cd21407; 1B_UPF1-like; 1.
DR CDD; cd18808; SF1_C_Upf1; 1.
DR CDD; cd21400; ZBD_UPF1-like; 1.
DR Gene3D; 3.40.50.300; -; 2.
DR InterPro; IPR045055; DNA2/NAM7-like.
DR InterPro; IPR041679; DNA2/NAM7-like_C.
DR InterPro; IPR041677; DNA2/NAM7_AAA_11.
DR InterPro; IPR006935; Helicase/UvrB_N.
DR InterPro; IPR014001; Helicase_ATP-bd.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR040812; UPF1_1B_dom.
DR InterPro; IPR018999; UPF1_CH/ZBD.
DR PANTHER; PTHR10887; PTHR10887; 1.
DR Pfam; PF13086; AAA_11; 1.
DR Pfam; PF13087; AAA_12; 1.
DR Pfam; PF04851; ResIII; 1.
DR Pfam; PF18141; UPF1_1B_dom; 1.
DR Pfam; PF09416; UPF1_Zn_bind; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
DR PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
DR PROSITE; PS51997; UPF1_CH_RICH; 1.
PE 1: Evidence at protein level;
KW ATP-binding; Cytoplasm; Helicase; Hydrolase; Metal-binding;
KW Nonsense-mediated mRNA decay; Nucleotide-binding; Phosphoprotein;
KW Plant defense; Reference proteome; RNA-binding; Zinc; Zinc-finger.
FT CHAIN 1..1254
FT /note="Regulator of nonsense transcripts 1 homolog"
FT /id="PRO_0000080721"
FT DOMAIN 132..291
FT /note="Upf1 CH-rich"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01341"
FT DOMAIN 497..629
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT REGION 1..106
FT /note="S/TQ motifs-rich, involved in the target transcript
FT degradation steps of nonsense-mediated decay (NMD)"
FT REGION 1..21
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 33..52
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 61..102
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 140..174
FT /note="C3H"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01341"
FT REGION 154..184
FT /note="CC/SHH/C"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01341"
FT REGION 202..232
FT /note="C4"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01341"
FT REGION 956..1096
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1013..1254
FT /note="S/TQ motifs-rich, involved in the target transcript
FT degradation steps of nonsense-mediated decay (NMD)"
FT REGION 1187..1254
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 33..51
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 996..1018
FT /note="Pro residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1049..1075
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 140
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01341"
FT BINDING 143
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01341"
FT BINDING 154
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01341"
FT BINDING 159
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01341"
FT BINDING 164
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01341"
FT BINDING 174
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01341"
FT BINDING 178
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01341"
FT BINDING 184
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01341"
FT BINDING 202
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01341"
FT BINDING 205
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01341"
FT BINDING 228
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01341"
FT BINDING 232
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01341"
FT BINDING 493
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q92900"
FT BINDING 513..517
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT BINDING 685
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q92900"
FT BINDING 722
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q92900"
FT BINDING 853
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q92900"
FT MUTAGEN 852
FT /note="R->C: Abolishes NMD."
FT /evidence="ECO:0000269|PubMed:22974464"
SQ SEQUENCE 1254 AA; 136868 MW; AE68846E70B27DC9 CRC64;
MDSQQSDLFD TASQPDTVAD EYTFLEFNTQ GDSEFDYQDF GSPTAWPTPS DSISIADVAD
RGEGGAAADH HSEASSPSSL SAGAGNGAKV GRGGVGGSGG VSSSSQVDAL AAGVGNLNFE
ETGDDDGFDY GKNDFTEHAC KYCGISNPAC VVRCNVASCR KWFCNSRGNT SGSHIVNHLV
RAKHKEVCLH RDSPLGETIL ECYNCGCRNV FLLGFISAKT DSVVVLLCRD PCLNVNALKD
MNWDLSQWCP LIDDRCFLPW LVKVPSEQEQ LRARQISAQQ INKIEELWKT NPDATLEDLE
KPGVDDEPQP VQPKYEDAYQ YQNVFAPLIK LEADYDKMMK ESQSKENLTV RWDIGLNKKR
VAYFVFPKEE NELRLVPGDE LRLRYSGDAV HPSWQSVGHV IKLTAQEEVA LELRANQGVP
IDVNHGFSVD FVWKSTSFDR MQGAMKNFAV DETSVSGYIY HQLLGHEVEA QMVRNTLPRR
FGVPGLPELN ASQVNAVKSV LQKPISLIQG PPGTGKTVTS AAIVYHMAKQ GQGQVLVCAP
SNVAVDQLAE KISATGLKVV RLCAKSREAV SSPVEYLTLH YQVRHLDTSE KSELHKLQQL
KDEQGELSSS DEKKYKNLKR ATEREITQSA DVICCTCVGA ADLRLSNFRF RQVLIDESTQ
ATEPECLIPL VLGVKQVVLV GDHCQLGPVI MCKKAARAGL AQSLFERLVT LGIKPIRLQV
QYRMHPALSE FPSNSFYEGT LQNGVTIIER QTTGIDFPWP VPNRPMFFYV QLGQEEISAS
GTSYLNRTEA ANVEKLVTAF LKSGVVPSQI GVITPYEGQR AYIVNYMARN GSLRQQLYKE
IEVASVDSFQ GREKDYIILS CVRSNEHQGI GFLNDPRRLN VALTRARYGI VILGNPKVLS
KQPLWNGLLT HYKEHECLVE GPLNNLKQSM VQFQKPRKIY NDRRLFYGGG AGMIGNDNFG
SGNPNADRRG SRGRAGGSYL PSGPPNGARP GLHPAGYPIP RVPLSPFPGG PPSQPYAIPT
RGPVGAVPHA PQPGNHGFGA GRGTSVGGHL PHQQATQHNV GTIGPSLNFP LDSPNSQPSP
GGPLSQPGYG SQAFRDGFSM GGISQDFLAD DIKSQGSHDP YNMADFATQA SPGGFAVDYA
TQGAHGAFPG NFMNQNSQGG YSRFSGINDF MSQEYMAHGG QGLFTQAGFI DSSQDDGQQN
PYGVNNPNLQ SQGLPNSLYS QPFAHYNTQP LNLSGPQQSQ PNQSSQNPKH PYNG
