PCFS4_ARATH
ID PCFS4_ARATH Reviewed; 808 AA.
AC Q0WPF2; Q8GW12; Q9ZS85;
DT 26-NOV-2014, integrated into UniProtKB/Swiss-Prot.
DT 05-SEP-2006, sequence version 1.
DT 25-MAY-2022, entry version 114.
DE RecName: Full=Polyadenylation and cleavage factor homolog 4 {ECO:0000305};
GN Name=PCFS4 {ECO:0000303|PubMed:18479511};
GN OrderedLocusNames=At4g04885 {ECO:0000312|Araport:AT4G04885};
GN ORFNames=T4B21.1 {ECO:0000312|EMBL:AAD03447.1};
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|EMBL:BAF00997.1};
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] (ISOFORM 2).
RC STRAIN=cv. Columbia;
RX PubMed=11910074; DOI=10.1126/science.1071006;
RA Seki M., Narusaka M., Kamiya A., Ishida J., Satou M., Sakurai T.,
RA Nakajima M., Enju A., Akiyama K., Oono Y., Muramatsu M., Hayashizaki Y.,
RA Kawai J., Carninci P., Itoh M., Ishii Y., Arakawa T., Shibata K.,
RA Shinagawa A., Shinozaki K.;
RT "Functional annotation of a full-length Arabidopsis cDNA collection.";
RL Science 296:141-145(2002).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP GENE FAMILY.
RX PubMed=15236668; DOI=10.1186/1471-2164-5-39;
RA Englbrecht C.C., Schoof H., Boehm S.;
RT "Conservation, diversification and expansion of C2H2 zinc finger proteins
RT in the Arabidopsis thaliana genome.";
RL BMC Genomics 5:39-39(2004).
RN [6]
RP HOMODIMER, INTERACTION WITH CPSF30; CLPS3; PCFS5 AND PCFS1, GENE FAMILY,
RP AND NOMENCLATURE.
RX PubMed=18479511; DOI=10.1186/1471-2164-9-220;
RA Hunt A.G., Xu R., Addepalli B., Rao S., Forbes K.P., Meeks L.R., Xing D.,
RA Mo M., Zhao H., Bandyopadhyay A., Dampanaboina L., Marion A.,
RA Von Lanken C., Li Q.Q.;
RT "Arabidopsis mRNA polyadenylation machinery: comprehensive analysis of
RT protein-protein interactions and gene expression profiling.";
RL BMC Genomics 9:220-220(2008).
RN [7]
RP FUNCTION, DISRUPTION PHENOTYPE, SUBCELLULAR LOCATION, INTERACTION WITH
RP CLPS3, TISSUE SPECIFICITY, AND DEVELOPMENTAL STAGE.
RC STRAIN=cv. Columbia;
RX PubMed=18298670; DOI=10.1111/j.1365-313x.2008.03455.x;
RA Xing D., Zhao H., Xu R., Li Q.Q.;
RT "Arabidopsis PCFS4, a homologue of yeast polyadenylation factor Pcf11p,
RT regulates FCA alternative processing and promotes flowering time.";
RL Plant J. 54:899-910(2008).
RN [8]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. Columbia;
RX PubMed=21364912; DOI=10.1371/journal.pone.0014719;
RA Zheng J., Xing D., Wu X., Shen Y., Kroll D.M., Ji G., Li Q.Q.;
RT "Ratio-based analysis of differential mRNA processing and expression of a
RT polyadenylation factor mutant pcfs4 using arabidopsis tiling microarray.";
RL PLoS ONE 6:E14719-E14719(2011).
CC -!- FUNCTION: Promotes flowering by suppressing FLC-mediated inhibition of
CC flowering through the regulation of FCA pre-mRNA alternative processing
CC (PubMed:18298670). Regulates mRNA maturation including alternative
CC polyadenylation, splicing or transcription initiation of stress-
CC associated genes (PubMed:21364912). {ECO:0000269|PubMed:18298670,
CC ECO:0000269|PubMed:21364912}.
CC -!- SUBUNIT: Homodimer. Forms a complex with cleavage and polyadenylation
CC specificity factor (CPSF) subunits CPSF30, CLPS3 and PCFS1.
CC {ECO:0000269|PubMed:18298670, ECO:0000269|PubMed:18479511}.
CC -!- INTERACTION:
CC Q0WPF2; Q9ZWJ9: ARR2; NbExp=3; IntAct=EBI-1775648, EBI-1101028;
CC Q0WPF2; Q9LNV5: At1g07360; NbExp=3; IntAct=EBI-1775648, EBI-2430550;
CC Q0WPF2; C0SUZ3: At1g35490; NbExp=3; IntAct=EBI-1775648, EBI-15192249;
CC Q0WPF2; Q9SR06: CLPS3; NbExp=3; IntAct=EBI-1775648, EBI-1775627;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:18298670}. Cytoplasm
CC {ECO:0000269|PubMed:18298670}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q0WPF2-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q0WPF2-2; Sequence=VSP_057255;
CC -!- TISSUE SPECIFICITY: Expressed in embryos, seedlings, roots, leaves and
CC flowers. {ECO:0000269|PubMed:18298670}.
CC -!- DEVELOPMENTAL STAGE: During embryogenesis, first observed at the heart
CC stage. Expressed through the whole developing embryo from the torpedo
CC stage. Disappears in the root tip of the mature embryo and in adult
CC plants. In seedlings, mostly present in the shoot apical meristem and
CC young leaves. In flowers, detected in sepals, stamens and pistils, but
CC not in petals. {ECO:0000269|PubMed:18298670}.
CC -!- DISRUPTION PHENOTYPE: Delayed flowering mediated by FLC under both
CC long-day and short-day conditions, but normal response to vernalization
CC treatment. Abnormal alternative polyadenylation-dependent FCA
CC expression profile of the known transcripts (PubMed:18298670). Global
CC differentially processed (DPG) and differentially expressed (DEG)
CC stress-associated genes due to alternative polyadenylation, splicing or
CC transcription initiation (PubMed:21364912).
CC {ECO:0000269|PubMed:18298670, ECO:0000269|PubMed:21364912}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAD03447.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AF118223; AAD03447.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002687; AEE82437.1; -; Genomic_DNA.
DR EMBL; AK119152; BAC43722.1; -; mRNA.
DR EMBL; AK229122; BAF00997.1; -; mRNA.
DR RefSeq; NP_680598.2; NM_148232.3. [Q0WPF2-1]
DR AlphaFoldDB; Q0WPF2; -.
DR SMR; Q0WPF2; -.
DR BioGRID; 11138; 39.
DR IntAct; Q0WPF2; 36.
DR STRING; 3702.AT4G04885.1; -.
DR PaxDb; Q0WPF2; -.
DR PRIDE; Q0WPF2; -.
DR ProteomicsDB; 236845; -. [Q0WPF2-1]
DR EnsemblPlants; AT4G04885.1; AT4G04885.1; AT4G04885. [Q0WPF2-1]
DR GeneID; 825827; -.
DR Gramene; AT4G04885.1; AT4G04885.1; AT4G04885. [Q0WPF2-1]
DR KEGG; ath:AT4G04885; -.
DR Araport; AT4G04885; -.
DR TAIR; locus:504955249; AT4G04885.
DR eggNOG; KOG2071; Eukaryota.
DR HOGENOM; CLU_006062_0_0_1; -.
DR InParanoid; Q0WPF2; -.
DR OMA; PANNRIF; -.
DR PhylomeDB; Q0WPF2; -.
DR PRO; PR:Q0WPF2; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q0WPF2; baseline and differential.
DR GO; GO:0005737; C:cytoplasm; IDA:TAIR.
DR GO; GO:0005849; C:mRNA cleavage factor complex; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; IDA:TAIR.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0003729; F:mRNA binding; IBA:GO_Central.
DR GO; GO:0000993; F:RNA polymerase II complex binding; IBA:GO_Central.
DR GO; GO:0009908; P:flower development; IEA:UniProtKB-KW.
DR GO; GO:0006379; P:mRNA cleavage; IEA:InterPro.
DR GO; GO:0006378; P:mRNA polyadenylation; IMP:TAIR.
DR GO; GO:0006397; P:mRNA processing; IMP:UniProtKB.
DR GO; GO:0009911; P:positive regulation of flower development; IMP:TAIR.
DR GO; GO:0006369; P:termination of RNA polymerase II transcription; IBA:GO_Central.
DR Gene3D; 1.25.40.90; -; 1.
DR InterPro; IPR006569; CID_dom.
DR InterPro; IPR008942; ENTH_VHS.
DR InterPro; IPR045154; PCF11-like.
DR InterPro; IPR013087; Znf_C2H2_type.
DR PANTHER; PTHR15921; PTHR15921; 1.
DR Pfam; PF04818; CID; 1.
DR SMART; SM00582; RPR; 1.
DR SUPFAM; SSF48464; SSF48464; 1.
DR PROSITE; PS51391; CID; 1.
DR PROSITE; PS00028; ZINC_FINGER_C2H2_1; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; Cytoplasm; Flowering; Metal-binding; mRNA processing;
KW Nucleus; Reference proteome; Zinc; Zinc-finger.
FT CHAIN 1..808
FT /note="Polyadenylation and cleavage factor homolog 4"
FT /id="PRO_0000431350"
FT DOMAIN 61..189
FT /note="CID"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00724"
FT ZN_FING 651..673
FT /note="C2H2-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00042"
FT REGION 1..32
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 192..212
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 246..293
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 785..808
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 9..23
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 192..206
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 246..284
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 791..808
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT VAR_SEQ 615..808
FT /note="Missing (in isoform 2)"
FT /id="VSP_057255"
SQ SEQUENCE 808 AA; 89228 MW; 03BABA1EE2B43515 CRC64;
MDSEKILNPR LVSINSTSRK GMSVELPQKP PPPPSLLDRF KALLNQREDE FGGGEEVLPP
SMDEIVQLYE VVLGELTFNS KPIITDLTII AGEQREHGEG IANAICTRIL EAPVEQKLPS
LYLLDSIVKN IGRDYGRYFS SRLPEVFCLA YRQAHPSLHP SMRHLFGTWS SVFPPPVLRK
IDMQLQLSSA ANQSSVGASE PSQPTRGIHV NPKYLRRLEP SAAENNLRGI NSSARVYGQN
SLGGYNDFED QLESPSSLSS TPDGFTRRSN DGANPSNQAF NYGMGRATSR DDEHMEWRRK
ENLGQGNDHE RPRALIDAYG VDTSKHVTIN KPIRDMNGMH SKMVTPWQNT EEEEFDWEDM
SPTLDRSRAG EFLRSSVPAL GSVRARPRVG NTSDFHLDSD IKNGVSHQLR ENWSLSQNYP
HTSNRVDTRA GKDLKVLASS VGLVSSNSEF GAPPFDSIQD VNSRFGRALP DGTWPHLSAR
GPNSLPVPSA HLHHLANPGN AMSNRLQGKP LYRPENQVSQ SHLNDMTQQN QMLVNYLPSS
SAMAPRPMQS LLTHVSHGYP PHGSTIRPSL SIQGGEAMHP LSSGVLSQIG ASNQPPGGAF
SGLIGSLMAQ GLISLNNQPA GQGPLGLEFD ADMLKIRNES AISALYGDLP RQCTTCGLRF
KCQEEHSKHM DWHVTKNRMS KNHKQNPSRK WFVSASMWLS GAEALGAEAV PGFLPTEPTT
EKKDDEDMAV PADEDQTSCA LCGEPFEDFY SDETEEWMYK GAVYMNAPEE STTDMDKSQL
GPIVHAKCRP ESNGGDMEEG SQRKKMRS
