PFD4_ARATH
ID PFD4_ARATH Reviewed; 129 AA.
AC Q9M4B5; Q84VV8;
DT 11-JAN-2001, integrated into UniProtKB/Swiss-Prot.
DT 31-MAY-2011, sequence version 3.
DT 03-AUG-2022, entry version 119.
DE RecName: Full=Prefoldin subunit 4 {ECO:0000303|PubMed:19825635};
DE AltName: Full=ABI3-interacting protein 3 {ECO:0000303|PubMed:10743655};
DE AltName: Full=Gene involved in microtubule biogenesis 3 {ECO:0000303|PubMed:19825635};
GN Name=PFD4 {ECO:0000303|PubMed:19825635};
GN Synonyms=AIP3 {ECO:0000303|PubMed:10743655},
GN GIM3 {ECO:0000303|PubMed:19825635};
GN OrderedLocusNames=At1g08780 {ECO:0000312|Araport:AT1G08780};
GN ORFNames=F22O13.27 {ECO:0000312|EMBL:AAF99774.1};
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=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 [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 NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
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 (FEB-2003) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NUCLEOTIDE SEQUENCE [MRNA] OF 4-129, AND INTERACTION WITH ABI3.
RC STRAIN=cv. Landsberg erecta;
RX PubMed=10743655; DOI=10.1046/j.1365-313x.2000.00663.x;
RA Kurup S., Jones H.D., Holdsworth M.J.;
RT "Interactions of the developmental regulator ABI3 with proteins identified
RT from developing Arabidopsis seeds.";
RL Plant J. 21:143-155(2000).
RN [6]
RP FUNCTION, DISRUPTION PHENOTYPE, AND INTERACTION WITH PFD6.
RC STRAIN=cv. Columbia;
RX PubMed=19004800; DOI=10.1073/pnas.0808652105;
RA Gu Y., Deng Z., Paredez A.R., DeBolt S., Wang Z.-Y., Somerville C.;
RT "Prefoldin 6 is required for normal microtubule dynamics and organization
RT in Arabidopsis.";
RL Proc. Natl. Acad. Sci. U.S.A. 105:18064-18069(2008).
RN [7]
RP FUNCTION, GENE FAMILY, AND NOMENCLATURE.
RX PubMed=19825635; DOI=10.1093/mp/ssp016;
RA Rodriguez-Milla M.A., Salinas J.;
RT "Prefoldins 3 and 5 play an essential role in Arabidopsis tolerance to salt
RT stress.";
RL Mol. Plant 2:526-534(2009).
RN [8]
RP FUNCTION, DISRUPTION PHENOTYPE, INDUCTION BY COLD, SUBCELLULAR LOCATION,
RP AND INTERACTION WITH HY5.
RC STRAIN=cv. Columbia;
RX PubMed=28412546; DOI=10.1016/j.molp.2017.03.012;
RA Perea-Resa C., Rodriguez-Milla M.A., Iniesto E., Rubio V., Salinas J.;
RT "Prefoldins negatively regulate cold acclimation in Arabidopsis thaliana by
RT promoting nuclear proteasome-mediated HY5 degradation.";
RL Mol. Plant 10:791-804(2017).
RN [9]
RP FUNCTION, DISRUPTION PHENOTYPE, INTERACTION WITH LSM8 AND HSP90, INDUCTION
RP BY COLD, AND REPRESSION BY GELDANAMYCIN.
RC STRAIN=cv. Columbia;
RX PubMed=32396196; DOI=10.1093/nar/gkaa354;
RA Esteve-Bruna D., Carrasco-Lopez C., Blanco-Tourinan N., Iserte J.,
RA Calleja-Cabrera J., Perea-Resa C., Urbez C., Carrasco P., Yanovsky M.J.,
RA Blazquez M.A., Salinas J., Alabadi D.;
RT "Prefoldins contribute to maintaining the levels of the spliceosome LSM2-8
RT complex through Hsp90 in Arabidopsis.";
RL Nucleic Acids Res. 48:6280-6293(2020).
CC -!- FUNCTION: Binds specifically to cytosolic chaperonin (c-CPN) and
CC transfers target proteins to it (PubMed:19825635). Binds to nascent
CC polypeptide chain and promotes folding in an environment in which there
CC are many competing pathways for nonnative proteins (PubMed:19825635).
CC Together with other chaperonins, contribute to the regulation of gene
CC expression by modulating the spliceosome function on pre-mRNA splicing
CC post-transcriptionally by acting as a co-chaperone of Hsp90 to control
CC levels of LSM8, especially in cold conditions (PubMed:32396196).
CC Required for microtubules (MTs) (MTs) organization and dynamicity
CC (PubMed:19004800, PubMed:28412546). Involved in the process leading to
CC microtubules dissociation in response to gibberellic acid (GA) probably
CC due to the DELLA proteins-mediated translocation of the prefoldin co-
CC chaperone complex from the cytoplasm to the nucleus (PubMed:28412546).
CC Prevents cold acclimation (e.g. 7 days at 4 degrees Celsius) in a DELLA
CC proteins-dependent manner by promoting nuclear proteasome-mediated HY5
CC degradation, thus modulating the expression of several genes and
CC reducing anthocyanin biosynthesis, but seems not involved in
CC constitutive freezing tolerance (PubMed:28412546).
CC {ECO:0000269|PubMed:19004800, ECO:0000269|PubMed:19825635,
CC ECO:0000269|PubMed:28412546, ECO:0000269|PubMed:32396196}.
CC -!- SUBUNIT: Heterohexamer of two PFD-alpha type and four PFD-beta type
CC subunits forming prefoldin co-chaperone complex (By similarity).
CC Interacts with ABI3 (via C-terminus) (PubMed:10743655). Interacts with
CC PFD6 (PubMed:19004800). Binds to HY5 in the nucleus and at low
CC temperature (e.g. at 4 degrees Celsius) (PubMed:28412546). Interacts
CC with LSM8, a specific subunit of the LSM2-8 complex, which is a core
CC component of the spliceosome (PubMed:32396196). Binds to HSP90 to
CC facilitate the formation of a larger complex made at least of HSP90,
CC PFD4 and LSM8 (PubMed:32396196). {ECO:0000250|UniProtKB:P46988,
CC ECO:0000269|PubMed:10743655, ECO:0000269|PubMed:19004800,
CC ECO:0000269|PubMed:28412546, ECO:0000269|PubMed:32396196}.
CC -!- INTERACTION:
CC Q9M4B5; Q01593: ABI3; NbExp=2; IntAct=EBI-2130809, EBI-1578892;
CC Q9M4B5; Q9LMM5: MPK11; NbExp=3; IntAct=EBI-2130809, EBI-2358699;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:28412546}. Nucleus
CC {ECO:0000269|PubMed:28412546}. Note=In the presence of gibberellic acid
CC (GA) and at room temperature, the prefoldin complex stays in the
CC cytoplasm and is functional (PubMed:28412546). But in the absence of GA
CC or in response to cold, the prefoldin complex is localized to the
CC nucleus in the presence of DELLA proteins, which severely compromises
CC alpha/beta-tubulin heterodimer availability, thus affecting
CC microtubules (MTs) organization (PubMed:28412546). This changing
CC subcellular localization follows a daily rhythm coordinated oscillation
CC (By similarity). {ECO:0000250|UniProtKB:P57742,
CC ECO:0000269|PubMed:28412546}.
CC -!- INDUCTION: Accumulates in response to cold (PubMed:28412546,
CC PubMed:32396196). Reduced levels upon treatment with geldanamycin
CC (GDA), a Hsp90 inhibitor (PubMed:32396196).
CC {ECO:0000269|PubMed:28412546, ECO:0000269|PubMed:32396196}.
CC -!- DISRUPTION PHENOTYPE: Hypersensitivity to oryzalin (a microtubule
CC inhibitor) (PubMed:19004800). Increased sensitivity to high salt
CC treatment (PubMed:32396196). Smaller plants due to reduced cells size
CC and associated with lower levels of both alpha and beta tubulin
CC subunits, as well as highly disorganized cortical microtubules (MTs)
CC (PubMed:28412546, PubMed:32396196). Increased capacity to tolerate
CC freezing temperatures upon acclimation (e.g. 7 days at 4 degrees
CC Celsius) associated with a continuous accumulation of HY5 in cold
CC conditions, characterized by a lower ubiquitination status
CC (PubMed:28412546). Reduced levels of LSM8 and of LSM2-8 complex via a
CC post-transcriptional process, especially in cold conditions (at protein
CC level) (PubMed:32396196). Slightly reduced production of U6 snRNA at
CC room temperature, but to higher extent in cold situation
CC (PubMed:32396196). Lower pre-mRNA splicing events and reduced
CC production of U6 snRNA in plants lacking PFD2, PFD4 and PFD6, probably
CC due to a reduced activity of the LSM2-8 complex (PubMed:32396196).
CC {ECO:0000269|PubMed:19004800, ECO:0000269|PubMed:28412546,
CC ECO:0000269|PubMed:32396196}.
CC -!- SIMILARITY: Belongs to the prefoldin subunit beta family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAF99774.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=CAB75510.1; Type=Miscellaneous discrepancy; Note=Intron retention.; Evidence={ECO:0000305};
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DR EMBL; AC003981; AAF99774.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002684; AEE28346.1; -; Genomic_DNA.
DR EMBL; BT004788; AAO44054.1; -; mRNA.
DR EMBL; AK227759; BAE99742.1; -; mRNA.
DR EMBL; AJ251088; CAB75510.1; ALT_SEQ; mRNA.
DR PIR; H86219; H86219.
DR RefSeq; NP_563827.1; NM_100752.4.
DR AlphaFoldDB; Q9M4B5; -.
DR SMR; Q9M4B5; -.
DR BioGRID; 22641; 11.
DR IntAct; Q9M4B5; 4.
DR STRING; 3702.AT1G08780.1; -.
DR iPTMnet; Q9M4B5; -.
DR PaxDb; Q9M4B5; -.
DR PRIDE; Q9M4B5; -.
DR ProteomicsDB; 236669; -.
DR EnsemblPlants; AT1G08780.1; AT1G08780.1; AT1G08780.
DR GeneID; 837400; -.
DR Gramene; AT1G08780.1; AT1G08780.1; AT1G08780.
DR KEGG; ath:AT1G08780; -.
DR Araport; AT1G08780; -.
DR TAIR; locus:2025655; AT1G08780.
DR eggNOG; KOG1760; Eukaryota.
DR HOGENOM; CLU_130032_0_0_1; -.
DR InParanoid; Q9M4B5; -.
DR OMA; KFGRAIN; -.
DR OrthoDB; 1459797at2759; -.
DR PRO; PR:Q9M4B5; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q9M4B5; baseline and differential.
DR Genevisible; Q9M4B5; AT.
DR GO; GO:0005737; C:cytoplasm; IDA:UniProtKB.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0016272; C:prefoldin complex; ISS:UniProtKB.
DR GO; GO:0051879; F:Hsp90 protein binding; IDA:UniProtKB.
DR GO; GO:0051082; F:unfolded protein binding; IEA:InterPro.
DR GO; GO:0071370; P:cellular response to gibberellin stimulus; ISS:UniProtKB.
DR GO; GO:0009631; P:cold acclimation; IMP:UniProtKB.
DR GO; GO:0043622; P:cortical microtubule organization; ISS:UniProtKB.
DR GO; GO:0006397; P:mRNA processing; IMP:UniProtKB.
DR GO; GO:0006457; P:protein folding; IMP:UniProtKB.
DR GO; GO:0009409; P:response to cold; IMP:UniProtKB.
DR GO; GO:0009651; P:response to salt stress; IMP:UniProtKB.
DR InterPro; IPR002777; PFD_beta-like.
DR InterPro; IPR016661; PFDN4.
DR PANTHER; PTHR21100; PTHR21100; 1.
DR Pfam; PF01920; Prefoldin_2; 1.
DR PIRSF; PIRSF016477; Prefoldin_subunit_4; 1.
PE 1: Evidence at protein level;
KW Chaperone; Coiled coil; Cytoplasm; Nucleus; Reference proteome.
FT CHAIN 1..129
FT /note="Prefoldin subunit 4"
FT /id="PRO_0000124845"
FT COILED 25..59
FT /evidence="ECO:0000255"
FT COILED 95..115
FT /evidence="ECO:0000255"
SQ SEQUENCE 129 AA; 14881 MW; 1562DF409E43884A CRC64;
MQQQGSKSGS EMEVTWEDQQ NINIFSRLNN RVHDLDDDIK SAKEKCENLE DAGNELILAD
EEMVRFQIGE VFAHVPRDDV ETKIEEMKEA TCKSLEKLEQ EKESIVTQMA ALKKVLYAKF
KDSINLEED
