PEP_ARATH
ID PEP_ARATH Reviewed; 495 AA.
AC Q9SZH4;
DT 04-MAR-2015, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 25-MAY-2022, entry version 146.
DE RecName: Full=RNA-binding KH domain-containing protein PEPPER {ECO:0000303|PubMed:16356489};
GN Name=PEP {ECO:0000303|PubMed:16356489};
GN OrderedLocusNames=At4g26000 {ECO:0000312|Araport:AT4G26000};
GN ORFNames=F20B18.110 {ECO:0000312|EMBL:CAB39665.1};
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 {ECO:0000312|Proteomes:UP000006548};
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617198; DOI=10.1038/47134;
RA Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T.,
RA Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B.,
RA Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M.,
RA de Simone V., Obermaier B., Mache R., Mueller M., Kreis M., Delseny M.,
RA Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D.,
RA Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J.,
RA Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B.,
RA Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J.,
RA Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R.,
RA Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P.,
RA Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S.,
RA Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C.,
RA Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J.,
RA Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S.,
RA Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A.,
RA Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M.,
RA Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D.,
RA Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S.,
RA Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R.,
RA Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M.,
RA Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E.,
RA Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P.,
RA Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K.,
RA Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K.,
RA de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K.,
RA Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M.,
RA Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G.,
RA Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K.,
RA Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
RA Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
RA Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H.,
RA Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B.,
RA Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J.,
RA Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K.,
RA O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N.,
RA Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A.,
RA Martienssen R., McCombie W.R.;
RT "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.";
RL Nature 402:769-777(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;
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, DISRUPTION PHENOTYPE, TISSUE SPECIFICITY, AND DEVELOPMENTAL
RP STAGE.
RC STRAIN=cv. Columbia, and cv. Wassilewskija-2;
RX PubMed=16356489; DOI=10.1016/j.ydbio.2005.10.037;
RA Ripoll J.J., Ferrandiz C., Martinez-Laborda A., Vera A.;
RT "PEPPER, a novel K-homology domain gene, regulates vegetative and gynoecium
RT development in Arabidopsis.";
RL Dev. Biol. 289:346-359(2006).
RN [5]
RP FUNCTION, DISRUPTION PHENOTYPE, AND SUBCELLULAR LOCATION.
RC STRAIN=cv. Columbia;
RX PubMed=19576878; DOI=10.1016/j.ydbio.2009.06.035;
RA Ripoll J.J., Rodriguez-Cazorla E., Gonzalez-Reig S., Andujar A.,
RA Alonso-Cantabrana H., Perez-Amador M.A., Carbonell J., Martinez-Laborda A.,
RA Vera A.;
RT "Antagonistic interactions between Arabidopsis K-homology domain genes
RT uncover PEPPER as a positive regulator of the central floral repressor
RT FLOWERING LOCUS C.";
RL Dev. Biol. 333:251-262(2009).
RN [6]
RP INTERACTION WITH HUA1 AND HEN4.
RX PubMed=25658099; DOI=10.1371/journal.pgen.1004983;
RA Rodriguez-Cazorla E., Ripoll J.J., Andujar A., Bailey L.J.,
RA Martinez-Laborda A., Yanofsky M.F., Vera A.;
RT "K-homology nuclear ribonucleoproteins regulate floral organ identity and
RT determinacy in arabidopsis.";
RL PLoS Genet. 11:E1004983-E1004983(2015).
CC -!- FUNCTION: Regulates vegetative and gynoecium development
CC (PubMed:16356489). In concert with HUA2, antagonizes FLK by positively
CC regulating FLC probably at transcriptional and post-transcriptional
CC levels, and thus acts as a negative regulator of flowering
CC (PubMed:19576878). {ECO:0000269|PubMed:16356489,
CC ECO:0000269|PubMed:19576878}.
CC -!- SUBUNIT: Interacts with HUA1 and HEN4. {ECO:0000269|PubMed:25658099}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:19576878}.
CC -!- TISSUE SPECIFICITY: Detected in roots, shoots, leaves, flowers and
CC fruits. {ECO:0000269|PubMed:16356489}.
CC -!- DEVELOPMENTAL STAGE: In seedlings, expressed in leaf primordia and
CC young developing leaves. Progressively circumscribed to the adaxial
CC side of developing leaves to become restricted to the veins in fully
CC expanded leaves. In roots, confined to the vasculature. Present in
CC floral buds and young developing flower organs. Accumulates in perianth
CC organs and stamens before being restricted to the vascular system in
CC later postanthesis stages. Strong expression throughout the young
CC pistil. Disappears from the apical stigma during postanthesis fruit
CC maturation. Detected in the style until later stages in fruit
CC development, mainly in style vasculature, but progressively fades away
CC from most of the ovary region. {ECO:0000269|PubMed:16356489}.
CC -!- DISRUPTION PHENOTYPE: Subtle morphological alterations in pep-2 and
CC pep-4 such as leaf alterations, phyllotactic errors and sporadic
CC presence of small fruits with multiple valves. Occasional asymmetry in
CC valve growth and unfused carpels (PubMed:16356489). Rescues the flk
CC mutant late-flowering phenotype with a concomitant decrease in FLC RNA
CC levels (PubMed:19576878). {ECO:0000269|PubMed:16356489,
CC ECO:0000269|PubMed:19576878}.
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DR EMBL; AL049483; CAB39665.1; -; Genomic_DNA.
DR EMBL; AL161564; CAB79455.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE85142.1; -; Genomic_DNA.
DR EMBL; AY056288; AAL07137.1; -; mRNA.
DR EMBL; AY099659; AAM20510.1; -; mRNA.
DR EMBL; AY114064; AAM45112.1; -; mRNA.
DR PIR; T04255; T04255.
DR RefSeq; NP_194330.1; NM_118733.4.
DR AlphaFoldDB; Q9SZH4; -.
DR SMR; Q9SZH4; -.
DR IntAct; Q9SZH4; 2.
DR STRING; 3702.AT4G26000.1; -.
DR iPTMnet; Q9SZH4; -.
DR PaxDb; Q9SZH4; -.
DR PRIDE; Q9SZH4; -.
DR ProteomicsDB; 236294; -.
DR EnsemblPlants; AT4G26000.1; AT4G26000.1; AT4G26000.
DR GeneID; 828706; -.
DR Gramene; AT4G26000.1; AT4G26000.1; AT4G26000.
DR KEGG; ath:AT4G26000; -.
DR Araport; AT4G26000; -.
DR TAIR; locus:2120755; AT4G26000.
DR eggNOG; KOG2190; Eukaryota.
DR HOGENOM; CLU_034604_2_0_1; -.
DR InParanoid; Q9SZH4; -.
DR OMA; CVFRMIV; -.
DR OrthoDB; 954970at2759; -.
DR PhylomeDB; Q9SZH4; -.
DR PRO; PR:Q9SZH4; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q9SZH4; baseline and differential.
DR Genevisible; Q9SZH4; AT.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0003729; F:mRNA binding; IBA:GO_Central.
DR GO; GO:0048467; P:gynoecium development; IMP:TAIR.
DR GO; GO:0009299; P:mRNA transcription; IMP:UniProtKB.
DR GO; GO:0048579; P:negative regulation of long-day photoperiodism, flowering; IMP:UniProtKB.
DR GO; GO:0048577; P:negative regulation of short-day photoperiodism, flowering; IMP:UniProtKB.
DR GO; GO:0010468; P:regulation of gene expression; IBA:GO_Central.
DR GO; GO:0006396; P:RNA processing; IMP:UniProtKB.
DR GO; GO:0048367; P:shoot system development; IMP:TAIR.
DR Gene3D; 3.30.1370.10; -; 1.
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; 3.
DR SUPFAM; SSF54791; SSF54791; 3.
DR PROSITE; PS50084; KH_TYPE_1; 3.
PE 1: Evidence at protein level;
KW Nucleus; Reference proteome; Repeat; RNA-binding; Transcription;
KW Transcription regulation.
FT CHAIN 1..495
FT /note="RNA-binding KH domain-containing protein PEPPER"
FT /id="PRO_0000432399"
FT DOMAIN 73..140
FT /note="KH 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00117"
FT DOMAIN 165..234
FT /note="KH 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00117"
FT DOMAIN 340..403
FT /note="KH 3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00117"
FT REGION 474..495
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 495 AA; 54025 MW; BCC855AC546AC143 CRC64;
MAAVADSVEN NGSINLPENE NLIPAGFSAA ALLDENSGAF PELNQPDSLA AAETTFPDTN
DSAEERWPGW PGDCVFRMIV PVTKVGAIIG RKGDFIKKMC EETRARIKVL DGPVNTPDRI
VLISGKEEPE AYMSPAMDAV LRVFRRVSGL PDNDDDDVQN AGSVFSSVRL LVASTQAINL
IGKQGSLIKS IVENSGASVR ILSEEETPFY AAQDERIVDL QGEALKILKA LEAIVGHLRR
FLVDHTVVPL FEKQYLARVS QTRQEEPLAE SKSSLHTISS NLMEPDFSLL ARREPLFLER
DSRVDSRVQP SGVSIYSQDP VLSARHSPGL ARVSSAFVTQ VSQTMQIPFS YAEDIIGVEG
ANIAYIRRRS GATITIKESP HPDQITVEIK GTTSQVQTAE QLIQEFIINH KEPVSVSGGY
ARIDSGYVPA YPPQLSNRQE PLPSTYMGTE PVQYRPTAYS QLGGPSTYTP TLTGQTYGSE
YRPASDVGGY SSYNL
