XRN4_ARATH
ID XRN4_ARATH Reviewed; 947 AA.
AC Q9FQ04; Q9SLI5;
DT 02-SEP-2008, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2001, sequence version 1.
DT 25-MAY-2022, entry version 128.
DE RecName: Full=5'-3' exoribonuclease 4;
DE EC=3.1.13.-;
DE AltName: Full=Protein ACC INSENSITIVE 1;
DE AltName: Full=Protein ETHYLENE INSENSITIVE 5;
DE AltName: Full=Protein EXORIBONUCLEASE 4;
GN Name=XRN4; Synonyms=AIN1, EIN5; OrderedLocusNames=At1g54490;
GN ORFNames=F20D21.30;
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], TISSUE SPECIFICITY, AND SUBCELLULAR LOCATION.
RX PubMed=11106401; DOI=10.1073/pnas.97.25.13985;
RA Kastenmayer J.P., Green P.J.;
RT "Novel features of the XRN-family in Arabidopsis: evidence that AtXRN4, one
RT of several orthologs of nuclear Xrn2p/Rat1p, functions in the cytoplasm.";
RL Proc. Natl. Acad. Sci. U.S.A. 97:13985-13990(2000).
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;
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 [5]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=15528448; DOI=10.1126/science.1101092;
RA Gazzani S., Lawrenson T., Woodward C., Headon D., Sablowski R.;
RT "A link between mRNA turnover and RNA interference in Arabidopsis.";
RL Science 306:1046-1048(2004).
RN [6]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=15260969; DOI=10.1016/j.molcel.2004.06.006;
RA Souret F.F., Kastenmayer J.P., Green P.J.;
RT "AtXRN4 degrades mRNA in Arabidopsis and its substrates include selected
RT miRNA targets.";
RL Mol. Cell 15:173-183(2004).
RN [7]
RP IDENTIFICATION, FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=16920797; DOI=10.1073/pnas.0605528103;
RA Olmedo G., Guo H., Gregory B.D., Nourizadeh S.D., Aguilar-Henonin L.,
RA Li H., An F., Guzman P., Ecker J.R.;
RT "ETHYLENE-INSENSITIVE5 encodes a 5'-->3' exoribonuclease required for
RT regulation of the EIN3-targeting F-box proteins EBF1/2.";
RL Proc. Natl. Acad. Sci. U.S.A. 103:13286-13293(2006).
RN [8]
RP FUNCTION, DISRUPTION PHENOTYPE, AND INDUCTION BY ETHYLENE.
RX PubMed=17085683; DOI=10.1105/tpc.106.046508;
RA Potuschak T., Vansiri A., Binder B.M., Lechner E., Vierstra R.D.,
RA Genschik P.;
RT "The exoribonuclease XRN4 is a component of the ethylene response pathway
RT in Arabidopsis.";
RL Plant Cell 18:3047-3057(2006).
CC -!- FUNCTION: Possesses 5'->3' exoribonuclease activity. Acts as an
CC endogenous post-transcriptional gene silencing (PTGS) suppressor.
CC Degrades miRNA target cleavage products that lack a 5'-cap structure.
CC Antagonizes the negative feedback regulation on EIN3 by promoting EBF1
CC and EBF2 mRNA decay, which consequently allows the accumulation of EIN3
CC protein to trigger the ethylene response. {ECO:0000269|PubMed:15260969,
CC ECO:0000269|PubMed:15528448, ECO:0000269|PubMed:16920797,
CC ECO:0000269|PubMed:17085683}.
CC -!- INTERACTION:
CC Q9FQ04; Q17TI5: BRX; NbExp=3; IntAct=EBI-25511549, EBI-4426649;
CC Q9FQ04; Q9LVG2: TOE2; NbExp=4; IntAct=EBI-25511549, EBI-4424568;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:11106401}.
CC -!- TISSUE SPECIFICITY: Expressed in roots, leaves, stems and flowers.
CC {ECO:0000269|PubMed:11106401}.
CC -!- INDUCTION: Not induced by ethylene. {ECO:0000269|PubMed:17085683}.
CC -!- DISRUPTION PHENOTYPE: Plants are viable with no apparent deleterious
CC phenotype. {ECO:0000269|PubMed:15260969, ECO:0000269|PubMed:15528448,
CC ECO:0000269|PubMed:16920797, ECO:0000269|PubMed:17085683}.
CC -!- SIMILARITY: Belongs to the 5'-3' exonuclease family. XRN2/RAT1
CC subfamily. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAD25627.1; Type=Erroneous gene model prediction; 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; AF286718; AAG40731.1; -; mRNA.
DR EMBL; AC005287; AAD25627.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002684; AEE33109.1; -; Genomic_DNA.
DR EMBL; AY064012; AAL36368.1; -; mRNA.
DR EMBL; AY091411; AAM14350.1; -; mRNA.
DR PIR; G96586; G96586.
DR RefSeq; NP_175851.1; NM_104327.4.
DR AlphaFoldDB; Q9FQ04; -.
DR SMR; Q9FQ04; -.
DR BioGRID; 27116; 2.
DR IntAct; Q9FQ04; 2.
DR STRING; 3702.AT1G54490.1; -.
DR iPTMnet; Q9FQ04; -.
DR PaxDb; Q9FQ04; -.
DR PRIDE; Q9FQ04; -.
DR ProteomicsDB; 242472; -.
DR EnsemblPlants; AT1G54490.1; AT1G54490.1; AT1G54490.
DR GeneID; 841891; -.
DR Gramene; AT1G54490.1; AT1G54490.1; AT1G54490.
DR KEGG; ath:AT1G54490; -.
DR Araport; AT1G54490; -.
DR TAIR; locus:2020073; AT1G54490.
DR eggNOG; KOG2044; Eukaryota.
DR HOGENOM; CLU_006038_1_0_1; -.
DR OMA; ETWEYIV; -.
DR OrthoDB; 685597at2759; -.
DR PhylomeDB; Q9FQ04; -.
DR PRO; PR:Q9FQ04; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q9FQ04; baseline and differential.
DR Genevisible; Q9FQ04; AT.
DR GO; GO:0010494; C:cytoplasmic stress granule; IDA:TAIR.
DR GO; GO:0005829; C:cytosol; IDA:TAIR.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0000932; C:P-body; IDA:UniProtKB.
DR GO; GO:0005844; C:polysome; IDA:UniProtKB.
DR GO; GO:0004534; F:5'-3' exoribonuclease activity; IMP:TAIR.
DR GO; GO:0003729; F:mRNA binding; IDA:TAIR.
DR GO; GO:0003723; F:RNA binding; IBA:GO_Central.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0051301; P:cell division; IMP:TAIR.
DR GO; GO:0070370; P:cellular heat acclimation; IMP:TAIR.
DR GO; GO:0031087; P:deadenylation-independent decapping of nuclear-transcribed mRNA; IMP:TAIR.
DR GO; GO:0010286; P:heat acclimation; IMP:UniProtKB.
DR GO; GO:0010587; P:miRNA catabolic process; IMP:TAIR.
DR GO; GO:0006402; P:mRNA catabolic process; IMP:UniProtKB.
DR GO; GO:0006397; P:mRNA processing; IEA:UniProtKB-KW.
DR GO; GO:0000956; P:nuclear-transcribed mRNA catabolic process; IBA:GO_Central.
DR GO; GO:0000291; P:nuclear-transcribed mRNA catabolic process, exonucleolytic; IMP:TAIR.
DR GO; GO:0010087; P:phloem or xylem histogenesis; IMP:TAIR.
DR GO; GO:0040029; P:regulation of gene expression, epigenetic; IMP:TAIR.
DR GO; GO:0009826; P:unidimensional cell growth; IMP:TAIR.
DR InterPro; IPR027073; 5_3_exoribonuclease.
DR InterPro; IPR004859; Put_53exo.
DR InterPro; IPR041412; Xrn1_helical.
DR InterPro; IPR017151; Xrn2/3/4.
DR InterPro; IPR001878; Znf_CCHC.
DR InterPro; IPR036875; Znf_CCHC_sf.
DR PANTHER; PTHR12341; PTHR12341; 2.
DR Pfam; PF17846; XRN_M; 2.
DR Pfam; PF03159; XRN_N; 1.
DR Pfam; PF00098; zf-CCHC; 1.
DR PIRSF; PIRSF037239; Exonuclease_Xrn2; 1.
DR SMART; SM00343; ZnF_C2HC; 1.
DR SUPFAM; SSF57756; SSF57756; 1.
DR PROSITE; PS50158; ZF_CCHC; 1.
PE 1: Evidence at protein level;
KW Cytoplasm; Exonuclease; Hydrolase; Metal-binding; mRNA processing;
KW Nuclease; Reference proteome; Zinc; Zinc-finger.
FT CHAIN 1..947
FT /note="5'-3' exoribonuclease 4"
FT /id="PRO_0000348956"
FT ZN_FING 263..280
FT /note="CCHC-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00047"
FT REGION 411..436
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 947 AA; 107778 MW; 7946FD3EC4BE755B CRC64;
MGVPAFYRWL ADRYPKSISD VVEEEPTDGG RGDLIPVDIT RPNPNGFEFD NLYLDMNGII
HPCFHPEGKP APATYDDVFK SMFEYIDHLF TLVRPRKILY LAIDGVAPRA KMNQQRSRRF
RAAKDAAEAE AEEERLRKDF EMEGQILSAK EKAETCDSNV ITPGTPFMAI LSVALQYYIQ
SRLNHNPGWR YVKVILSDSN VPGEGEHKIM SYIRLQRNLP GFDPNTRHCL YGLDADLIML
SLATHEVHFS ILREVITYPG QQEKCFVCGQ TGHFASDCPG KSGSNNAAAD IPIHKKKYQF
LNIWVLREYL QYELAIPDPP FMINFERIID DFVFLCFFVG NDFLPHMPTL EIREGAINLL
MHVYRKEFTA MGGYLTDSGE VLLDRVEHFI QAVAVNEDKI FQKRTRIKQS MDNNEEMKQR
SRRDPSEVPP EPIDDKIKLG EPGYKERYYA EKFSTTNPEE TEQIKQDMVL KYVEGLCWVC
RYYYQGVCSW QWFYPYHYAP FASDLKNLPD LEITFFIGEP FKPFDQLMGT LPAASSNALP
GEYRKLMTDP SSPILKFYPA DFELDMNGKR FAWQGIAKLP FIEEKLLLAA TRKLEETLTV
EEQQRNSVML DLLYVHPAHP LGQRILQYYH FYQHMPPHEC LPWMIDPNSS QGMNGFLWFS
ERNGFQTRVD SPVNGLPCIE QNRALNVTYL CPAKHSHISE PPRGAIIPDK ILTSVDIKPF
PPLWHEDNSN RRRQARDRPQ VVGAIAGPSL GEAAHRLIKN TLNMKSSTGA ASGLIDPNGY
YRNVPGNYSY GGVNRPRAPG PSPYRKAYDD DSSYYYGKYN NSTQGTFNNG PRYPYPSNGS
QDYNRNYNSK IVAEQHNRGG LGAGMSGLSI EDNGRSKQLY SSYTEAANAN LNPLPSPPTQ
WIGTQPGGNF VGGYYRDGVG YSETNGKSVK KVIYQAKTQP SHRGANL
