RCF3_ARATH
ID RCF3_ARATH Reviewed; 652 AA.
AC Q8W4B1; Q9LVU6;
DT 18-JAN-2017, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2002, sequence version 1.
DT 25-MAY-2022, entry version 134.
DE RecName: Full=RNA-binding KH domain-containing protein RCF3 {ECO:0000305|PubMed:23087326};
DE AltName: Full=Protein ENHANCED STRESS RESPONSE 1 {ECO:0000303|PubMed:25985302};
DE AltName: Full=Protein HIGH OSMOTIC STRESS GENE EXPRESSION 5 {ECO:0000303|PubMed:24146632};
DE AltName: Full=Protein REGULATOR OF CBF GENE EXPRESSION 3 {ECO:0000303|PubMed:23087326};
DE AltName: Full=Protein SHINY 1 {ECO:0000303|PubMed:23874224};
GN Name=RCF3 {ECO:0000303|PubMed:23087326};
GN Synonyms=ESR1 {ECO:0000303|PubMed:25985302},
GN HOS5 {ECO:0000303|PubMed:24146632}, SHI1 {ECO:0000303|PubMed:23874224};
GN OrderedLocusNames=At5g53060 {ECO:0000312|Araport:AT5G53060};
GN ORFNames=MNB8.12 {ECO:0000312|EMBL:BAA97146.1};
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=10718197; DOI=10.1093/dnares/7.1.31;
RA Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Kotani H.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. X. Sequence
RT features of the regions of 3,076,755 bp covered by sixty P1 and TAC
RT clones.";
RL DNA Res. 7:31-63(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.
RX PubMed=10504578; DOI=10.1046/j.1365-313x.1999.00558.x;
RA Xiong L., Ishitani M., Lee H., Zhu J.K.;
RT "HOS5-a negative regulator of osmotic stress-induced gene expression in
RT Arabidopsis thaliana.";
RL Plant J. 19:569-578(1999).
RN [5]
RP FUNCTION, SUBCELLULAR LOCATION, INDUCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=23087326; DOI=10.1093/mp/sss119;
RA Guan Q., Wen C., Zeng H., Zhu J.;
RT "A KH domain-containing putative RNA-binding protein is critical for heat
RT stress-responsive gene regulation and thermotolerance in Arabidopsis.";
RL Mol. Plant 6:386-395(2013).
RN [6]
RP FUNCTION, INTERACTION WITH CPL1, TISSUE SPECIFICITY, INDUCTION, MUTAGENESIS
RP OF GLU-389, AND DISRUPTION PHENOTYPE.
RX PubMed=23874224; DOI=10.1371/journal.pgen.1003625;
RA Jiang J., Wang B., Shen Y., Wang H., Feng Q., Shi H.;
RT "The arabidopsis RNA binding protein with K homology motifs, SHINY1,
RT interacts with the C-terminal domain phosphatase-like 1 (CPL1) to repress
RT stress-inducible gene expression.";
RL PLoS Genet. 9:E1003625-E1003625(2013).
RN [7]
RP FUNCTION, INTERACTION WITH CPL1; RS40 AND RS41, SUBCELLULAR LOCATION,
RP TISSUE SPECIFICITY, MUTAGENESIS OF GLY-233, AND DISRUPTION PHENOTYPE.
RX PubMed=24146632; DOI=10.1371/journal.pgen.1003875;
RA Chen T., Cui P., Chen H., Ali S., Zhang S., Xiong L.;
RT "A KH-domain RNA-binding protein interacts with FIERY2/CTD phosphatase-like
RT 1 and splicing factors and is important for pre-mRNA splicing in
RT Arabidopsis.";
RL PLoS Genet. 9:E1003875-E1003875(2013).
RN [8]
RP IDENTIFICATION BY MASS SPECTROMETRY, INTERACTION WITH CPL1, AND SUBCELLULAR
RP LOCATION.
RX PubMed=24303021; DOI=10.1371/journal.pone.0080509;
RA Jeong I.S., Fukudome A., Aksoy E., Bang W.Y., Kim S., Guan Q., Bahk J.D.,
RA May K.A., Russell W.K., Zhu J., Koiwa H.;
RT "Regulation of abiotic stress signalling by Arabidopsis C-terminal domain
RT phosphatase-like 1 requires interaction with a k-homology domain-containing
RT protein.";
RL PLoS ONE 8:E80509-E80509(2013).
RN [9]
RP FUNCTION, AND INTERACTION WITH DRB1/HYL1 AND SE.
RX PubMed=26227967; DOI=10.1093/nar/gkv751;
RA Chen T., Cui P., Xiong L.;
RT "The RNA-binding protein HOS5 and serine/arginine-rich proteins RS40 and
RT RS41 participate in miRNA biogenesis in Arabidopsis.";
RL Nucleic Acids Res. 43:8283-8298(2015).
RN [10]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=25985302; DOI=10.1371/journal.pone.0126978;
RA Thatcher L.F., Kamphuis L.G., Hane J.K., Onate-Sanchez L., Singh K.B.;
RT "The Arabidopsis KH-domain RNA-binding protein ESR1 functions in components
RT of jasmonate signalling, unlinking growth restraint and resistance to
RT stress.";
RL PLoS ONE 10:E0126978-E0126978(2015).
RN [11]
RP FUNCTION, AND INTERACTION WITH CPL1 AND CPL2.
RX PubMed=26512101; DOI=10.1073/pnas.1512865112;
RA Karlsson P., Christie M.D., Seymour D.K., Wang H., Wang X., Hagmann J.,
RA Kulcheski F., Manavella P.A.;
RT "KH domain protein RCF3 is a tissue-biased regulator of the plant miRNA
RT biogenesis cofactor HYL1.";
RL Proc. Natl. Acad. Sci. U.S.A. 112:14096-14101(2015).
CC -!- FUNCTION: Acts as negative regulator of osmotic stress-induced gene
CC expression (PubMed:10504578). Involved in the regulation of
CC thermotolerance responses under heat stress. Functions as an upstream
CC regulator of heat stress transcription factor (HSF) genes. Negatively
CC regulates HSFA1A, HSFA1B AND HSFA1D, but positively controls the
CC expression of HSFA1E, HSFA3, HSFA9, HSFB3, and DREB2C
CC (PubMed:23087326). Forms a complex with CPL1 that modulates co-
CC transcriptional processes such as mRNA capping and polyadenylation, and
CC functions to repress stress-inducible gene expression
CC (PubMed:23874224). Regulates pre-mRNA processing under salt stress
CC (PubMed:24146632). Involved in primary miRNA processing and pri-miRNA
CC biogenesis (PubMed:26227967, PubMed:26512101). Binds both intronless
CC and intron-containing pri-miRNAs (PubMed:26227967). Acts as a regulator
CC of biotic stress response gene expression and basal JA-mediated
CC responses involved in defense. Acts as negative regulator of resistance
CC to the fungal pathogen Fusarium oxysporum (PubMed:25985302).
CC {ECO:0000269|PubMed:10504578, ECO:0000269|PubMed:23087326,
CC ECO:0000269|PubMed:23874224, ECO:0000269|PubMed:24146632,
CC ECO:0000269|PubMed:25985302, ECO:0000269|PubMed:26227967,
CC ECO:0000269|PubMed:26512101}.
CC -!- SUBUNIT: Homodimer (PubMed:24146632). Interacts with CPL1
CC (PubMed:23874224, PubMed:24146632, PubMed:24303021, PubMed:26512101).
CC Interacts with RS40 and RS41 (PubMed:24146632). Interacts with
CC DRB1/HYL1 and SE (PubMed:26227967). Interacts with CPL2
CC (PubMed:26512101). {ECO:0000269|PubMed:23874224,
CC ECO:0000269|PubMed:24146632, ECO:0000269|PubMed:24303021,
CC ECO:0000269|PubMed:26227967, ECO:0000269|PubMed:26512101}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:23087326,
CC ECO:0000269|PubMed:23874224, ECO:0000269|PubMed:24146632,
CC ECO:0000269|PubMed:24303021}. Nucleus speckle
CC {ECO:0000269|PubMed:24146632}. Note=Localizes predominantly in nuclear
CC speckles. {ECO:0000269|PubMed:24146632}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=1;
CC Comment=A number of isoforms are produced. According to EST
CC sequences. {ECO:0000305};
CC Name=1;
CC IsoId=Q8W4B1-1; Sequence=Displayed;
CC -!- TISSUE SPECIFICITY: Expressed in roots, cotyledons, leaves, flowers and
CC siliques. {ECO:0000269|PubMed:23874224, ECO:0000269|PubMed:24146632}.
CC -!- INDUCTION: Transiently down-regulated by heat stress (PubMed:23087326).
CC Down-regulated by salt stress, osmotic shock, treatment with lithium or
CC abscisic acid (ABA), and low or high pH (PubMed:23874224).
CC {ECO:0000269|PubMed:23087326, ECO:0000269|PubMed:23874224}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype under normal growth
CC conditions (PubMed:23087326, PubMed:23874224, PubMed:24146632,
CC PubMed:25985302). Mutant seedlings show increased tolerance to heat
CC stress (PubMed:23087326, PubMed:25985302). Mutant seedlings show
CC increased sensitivity to salt stress and abscisic acid (ABA)
CC (PubMed:24146632). Mutant plants exhibit increased resistance to the
CC fungal pathogen Fusarium oxysporum (PubMed:25985302).
CC {ECO:0000269|PubMed:23087326, ECO:0000269|PubMed:23874224,
CC ECO:0000269|PubMed:24146632, ECO:0000269|PubMed:25985302}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAA97146.1; 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; AB018116; BAA97146.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002688; AED96298.1; -; Genomic_DNA.
DR EMBL; AY062686; AAL32764.1; -; mRNA.
DR EMBL; BT008402; AAP37761.1; -; mRNA.
DR RefSeq; NP_200118.3; NM_124685.4. [Q8W4B1-1]
DR AlphaFoldDB; Q8W4B1; -.
DR SMR; Q8W4B1; -.
DR IntAct; Q8W4B1; 10.
DR STRING; 3702.AT5G53060.1; -.
DR iPTMnet; Q8W4B1; -.
DR PaxDb; Q8W4B1; -.
DR PRIDE; Q8W4B1; -.
DR ProteomicsDB; 225942; -. [Q8W4B1-1]
DR EnsemblPlants; AT5G53060.1; AT5G53060.1; AT5G53060. [Q8W4B1-1]
DR GeneID; 835386; -.
DR Gramene; AT5G53060.1; AT5G53060.1; AT5G53060. [Q8W4B1-1]
DR KEGG; ath:AT5G53060; -.
DR Araport; AT5G53060; -.
DR TAIR; locus:2168367; AT5G53060.
DR eggNOG; KOG2190; Eukaryota.
DR HOGENOM; CLU_018025_3_0_1; -.
DR InParanoid; Q8W4B1; -.
DR OMA; KRYYYDQ; -.
DR PhylomeDB; Q8W4B1; -.
DR PRO; PR:Q8W4B1; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q8W4B1; baseline and differential.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0010445; C:nuclear dicing body; IDA:TAIR.
DR GO; GO:0016607; C:nuclear speck; IEA:UniProtKB-SubCell.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0003729; F:mRNA binding; IBA:GO_Central.
DR GO; GO:0070878; F:primary miRNA binding; IDA:TAIR.
DR GO; GO:0010286; P:heat acclimation; IMP:TAIR.
DR GO; GO:0009867; P:jasmonic acid mediated signaling pathway; IMP:TAIR.
DR GO; GO:0006397; P:mRNA processing; IEA:UniProtKB-KW.
DR GO; GO:0031053; P:primary miRNA processing; IMP:TAIR.
DR GO; GO:1900150; P:regulation of defense response to fungus; IMP:TAIR.
DR GO; GO:0010468; P:regulation of gene expression; IMP:TAIR.
DR GO; GO:0006970; P:response to osmotic stress; IMP:TAIR.
DR GO; GO:0008380; P:RNA splicing; IEA:UniProtKB-KW.
DR Gene3D; 3.30.1370.10; -; 3.
DR InterPro; IPR004087; KH_dom.
DR InterPro; IPR004088; KH_dom_type_1.
DR InterPro; IPR036612; KH_dom_type_1_sf.
DR Pfam; PF00013; KH_1; 3.
DR SMART; SM00322; KH; 5.
DR SUPFAM; SSF54791; SSF54791; 5.
DR PROSITE; PS50084; KH_TYPE_1; 4.
PE 1: Evidence at protein level;
KW Alternative splicing; mRNA processing; mRNA splicing; Nucleus;
KW Reference proteome; Repeat; RNA-binding.
FT CHAIN 1..652
FT /note="RNA-binding KH domain-containing protein RCF3"
FT /id="PRO_0000438737"
FT DOMAIN 67..139
FT /note="KH 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00117"
FT DOMAIN 175..245
FT /note="KH 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00117"
FT DOMAIN 324..391
FT /note="KH 3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00117"
FT DOMAIN 408..476
FT /note="KH 4"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00117"
FT DOMAIN 576..640
FT /note="KH 5"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00117"
FT REGION 1..63
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 253..307
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..22
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 287..307
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MUTAGEN 233
FT /note="G->S: In hos5-1; increased sensitivity to salt
FT stress."
FT /evidence="ECO:0000269|PubMed:24146632"
FT MUTAGEN 389
FT /note="E->K: In shi1; increased sensitivity to cold
FT stress."
FT /evidence="ECO:0000269|PubMed:23874224"
SQ SEQUENCE 652 AA; 71345 MW; 62D1AB522C5B2546 CRC64;
MERSRSKRNY HYDQDYDGDS MPRSKPRYNN NYHFGGGGGG NNRYRGGGGG GGGNGRPSKS
HPETMATTTY RILCHDAKAG GVIGKSGTII KSIRQHTGAW INVHELVPGD AERIIEISDN
RRRDPDGRMP SFSPAQEALF SVHDRILESE AQFGYGGPPP EEEEDYGGVR PGGGRVVTRL
VVSRMHVGCL LGKGGKIIEQ MRIETKTHIR ILPRESNLPR CVSLSEEIVQ IVGELNAVKN
ALAIVSSRLR ESQHRDRSNF QGRSHSPERS FAAAGDDYMP QLRRQSSDRF PRGNFRNNNF
SSRQSNYAEE APAVPVGENV YSEELVFQIL CPADKIVRVV GESQGIIDLL QNEIGVDVRV
SDPVAGSDEQ IITISSEEAP DDPFFPAQEA LLHIQTQIID LIPDKDNLIT TRLLVPSRDS
ICLEGKAGSV SEISRLTGTS VQILAREEIP RCASINDVVI QITGEIRAAR EALVELTLLL
RSHMFKELSQ KETPPASTST TGPLEGVAGV MEVASSNNTI QSREGPTSSN LNLQQVSTIL
PQFKEGFGSV AKAGESEHRE EVPVTTSRMA VPLVTRSTLE VVLPEAVVPK LVTKSRNKLA
QISEWSGASV TIVEDRPEET QNIIRISGTP EQAERAQSLL QGFILSIQED GP
