SPX4_ORYSJ
ID SPX4_ORYSJ Reviewed; 320 AA.
AC Q10B79; A0A0P0W5I5; A3APA3; Q0DM53; Q10B78; Q8SAX5;
DT 05-OCT-2010, integrated into UniProtKB/Swiss-Prot.
DT 22-AUG-2006, sequence version 1.
DT 03-AUG-2022, entry version 79.
DE RecName: Full=SPX domain-containing protein 4;
DE AltName: Full=Protein SPX DOMAIN GENE 4;
DE Short=OsSPX4;
GN Name=SPX4; OrderedLocusNames=Os03g0827500, LOC_Os03g61200;
GN ORFNames=OsJ_13205, OSJNBa0010E04.24;
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16109971; DOI=10.1101/gr.3869505;
RG The rice chromosome 3 sequencing consortium;
RA Buell C.R., Yuan Q., Ouyang S., Liu J., Zhu W., Wang A., Maiti R., Haas B.,
RA Wortman J., Pertea M., Jones K.M., Kim M., Overton L., Tsitrin T.,
RA Fadrosh D., Bera J., Weaver B., Jin S., Johri S., Reardon M., Webb K.,
RA Hill J., Moffat K., Tallon L., Van Aken S., Lewis M., Utterback T.,
RA Feldblyum T., Zismann V., Iobst S., Hsiao J., de Vazeille A.R.,
RA Salzberg S.L., White O., Fraser C.M., Yu Y., Kim H., Rambo T., Currie J.,
RA Collura K., Kernodle-Thompson S., Wei F., Kudrna K., Ammiraju J.S.S.,
RA Luo M., Goicoechea J.L., Wing R.A., Henry D., Oates R., Palmer M.,
RA Pries G., Saski C., Simmons J., Soderlund C., Nelson W., de la Bastide M.,
RA Spiegel L., Nascimento L., Huang E., Preston R., Zutavern T., Palmer L.,
RA O'Shaughnessy A., Dike S., McCombie W.R., Minx P., Cordum H., Wilson R.,
RA Jin W., Lee H.R., Jiang J., Jackson S.;
RT "Sequence, annotation, and analysis of synteny between rice chromosome 3
RT and diverged grass species.";
RL Genome Res. 15:1284-1291(2005).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT "The genomes of Oryza sativa: a history of duplications.";
RL PLoS Biol. 3:266-281(2005).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12869764; DOI=10.1126/science.1081288;
RG The rice full-length cDNA consortium;
RT "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT japonica rice.";
RL Science 301:376-379(2003).
RN [7]
RP TISSUE SPECIFICITY, LACK OF INDUCTION BY PHOSPHATE, AND SUBCELLULAR
RP LOCATION.
RX PubMed=19566645; DOI=10.1111/j.1744-7909.2009.00834.x;
RA Wang Z., Hu H., Huang H., Duan K., Wu Z., Wu P.;
RT "Regulation of OsSPX1 and OsSPX3 on expression of OsSPX domain genes and
RT Pi-starvation signaling in rice.";
RL J. Integr. Plant Biol. 51:663-674(2009).
RN [8]
RP GENE FAMILY, NOMENCLATURE, AND INDUCTION BY COLD.
RX PubMed=19508276; DOI=10.1111/j.1467-7652.2009.00423.x;
RA Zhao L., Liu F., Xu W., Di C., Zhou S., Xue Y., Yu J., Su Z.;
RT "Increased expression of OsSPX1 enhances cold/subfreezing tolerance in
RT tobacco and Arabidopsis thaliana.";
RL Plant Biotechnol. J. 7:550-561(2009).
RN [9]
RP INTERACTION WITH PHR2, DISRUPTION PHENOTYPE, LACK OF INDUCTION BY
RP PHOSPHATE, TISSUE SPECIFICITY, DEGRADATION, SUBCELLULAR LOCATION, AND
RP SUBUNIT.
RX PubMed=24692424; DOI=10.1105/tpc.114.123208;
RA Lv Q., Zhong Y., Wang Y., Wang Z., Zhang L., Shi J., Wu Z., Liu Y., Mao C.,
RA Yi K., Wu P.;
RT "SPX4 negatively regulates phosphate signaling and homeostasis through its
RT interaction with PHR2 in Rice.";
RL Plant Cell 26:1586-1597(2014).
RN [10]
RP FUNCTION, MUTAGENESIS OF TYR-25; LYS-29 AND LYS-155, AND INTERACTION WITH
RP PHR2.
RX PubMed=27080106; DOI=10.1126/science.aad9858;
RA Wild R., Gerasimaite R., Jung J.Y., Truffault V., Pavlovic I., Schmidt A.,
RA Saiardi A., Jessen H.J., Poirier Y., Hothorn M., Mayer A.;
RT "Control of eukaryotic phosphate homeostasis by inositol polyphosphate
RT sensor domains.";
RL Science 352:986-990(2016).
RN [11]
RP INTERACTION WITH BHLH6.
RX PubMed=33128314; DOI=10.1111/tpj.15061;
RA He Q., Lu H., Guo H., Wang Y., Zhao P., Li Y., Wang F., Xu J., Mo X.,
RA Mao C.;
RT "OsbHLH6 interacts with OsSPX4 and regulates the phosphate-starvation
RT response in rice.";
RL Plant J. 105:649-667(2021).
CC -!- FUNCTION: Inositol polyphosphate sensor that associates with
CC transcription factors to regulate Pi starvation responses
CC (PubMed:27080106). The SPX domain provides a basic binding surface for
CC inositol polyphosphate signaling molecules (PubMed:27080106). Interacts
CC with PHR2 to inhibits its translocation to the nucleus and repress its
CC DNA-binding activity, and then negatively regulate Pi signaling
CC (PubMed:24692424). {ECO:0000269|PubMed:24692424,
CC ECO:0000269|PubMed:27080106}.
CC -!- SUBUNIT: Homodimer (PubMed:24692424). Interacts (via N-terminus) with
CC PHR2 (via C-terminus) in the presence of inositol polyphosphate
CC (PubMed:24692424, PubMed:27080106). Interacts with BHLH6
CC (PubMed:33128314). {ECO:0000269|PubMed:24692424,
CC ECO:0000269|PubMed:27080106, ECO:0000269|PubMed:33128314}.
CC -!- INTERACTION:
CC Q10B79-1; Q6F6A2: PHR; NbExp=2; IntAct=EBI-16205145, EBI-16205114;
CC -!- SUBCELLULAR LOCATION: Membrane {ECO:0000269|PubMed:19566645}. Nucleus
CC {ECO:0000269|PubMed:24692424}. Cytoplasm {ECO:0000269|PubMed:24692424}.
CC Note=Unlike PubMed:19566645, PubMed:24692424 cannot find a membrane
CC localization.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q10B79-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q10B79-2; Sequence=VSP_039757, VSP_039758;
CC -!- TISSUE SPECIFICITY: Widely expressed (PubMed:19566645). Detected in
CC root cells, with the exception of epidermis, and in mesophyll and
CC vascular bundles in leaves (PubMed:24692424).
CC {ECO:0000269|PubMed:19566645, ECO:0000269|PubMed:24692424}.
CC -!- INDUCTION: Up-regulated during cold stress (PubMed:19508276). Not
CC regulated by Pi-starvation (PubMed:19566645, PubMed:24692424).
CC {ECO:0000269|PubMed:19508276, ECO:0000269|PubMed:19566645,
CC ECO:0000269|PubMed:24692424}.
CC -!- PTM: Degraded under Pi starvation conditions through the ubiquitin/26S
CC proteasome pathway. {ECO:0000269|PubMed:24692424}.
CC -!- DISRUPTION PHENOTYPE: Growth inihibition, Pi accumulation in shoots and
CC up-regulation of phosphate starvation-induced (PSI) genes downstream of
CC PHR2 under high phosphate conditions. {ECO:0000269|PubMed:24692424}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAF13685.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=EAZ29142.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AC096687; AAL79759.1; -; Genomic_DNA.
DR EMBL; DP000009; ABF99664.1; -; Genomic_DNA.
DR EMBL; DP000009; ABF99665.1; -; Genomic_DNA.
DR EMBL; AP008209; BAF13685.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AP014959; BAS87167.1; -; Genomic_DNA.
DR EMBL; CM000140; EAZ29142.1; ALT_INIT; Genomic_DNA.
DR EMBL; AK066364; -; NOT_ANNOTATED_CDS; mRNA.
DR RefSeq; XP_015630412.1; XM_015774926.1. [Q10B79-1]
DR AlphaFoldDB; Q10B79; -.
DR SMR; Q10B79; -.
DR DIP; DIP-62041N; -.
DR IntAct; Q10B79; 1.
DR STRING; 4530.OS03T0827500-01; -.
DR PaxDb; Q10B79; -.
DR PRIDE; Q10B79; -.
DR EnsemblPlants; Os03t0827500-01; Os03t0827500-01; Os03g0827500. [Q10B79-1]
DR GeneID; 4334647; -.
DR Gramene; Os03t0827500-01; Os03t0827500-01; Os03g0827500. [Q10B79-1]
DR KEGG; osa:4334647; -.
DR eggNOG; KOG1161; Eukaryota.
DR InParanoid; Q10B79; -.
DR OMA; AAMRTIQ; -.
DR OrthoDB; 1345784at2759; -.
DR Proteomes; UP000000763; Chromosome 3.
DR Proteomes; UP000007752; Chromosome 3.
DR Proteomes; UP000059680; Chromosome 3.
DR ExpressionAtlas; Q10B79; baseline and differential.
DR Genevisible; Q10B79; OS.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0016020; C:membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0070417; P:cellular response to cold; IEP:UniProtKB.
DR GO; GO:0016036; P:cellular response to phosphate starvation; IEA:InterPro.
DR InterPro; IPR004331; SPX_dom.
DR InterPro; IPR031142; SPX_prot.
DR PANTHER; PTHR45978; PTHR45978; 1.
DR PANTHER; PTHR45978:SF7; PTHR45978:SF7; 1.
DR Pfam; PF03105; SPX; 2.
DR PROSITE; PS51382; SPX; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; Cytoplasm; Membrane; Nucleus; Reference proteome.
FT CHAIN 1..320
FT /note="SPX domain-containing protein 4"
FT /id="PRO_0000398353"
FT DOMAIN 1..170
FT /note="SPX"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00714"
FT REGION 209..233
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 275..320
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT VAR_SEQ 149..157
FT /note="LVKILKKYD -> ELIKPSWLV (in isoform 2)"
FT /evidence="ECO:0000305"
FT /id="VSP_039757"
FT VAR_SEQ 158..320
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000305"
FT /id="VSP_039758"
FT MUTAGEN 25
FT /note="Y->F: In PBC; loss of inositol polyphosphate
FT binding; when associated with A-29 and A-155."
FT /evidence="ECO:0000269|PubMed:27080106"
FT MUTAGEN 29
FT /note="K->A: In PBC; loss of inositol polyphosphate
FT binding; when associated with F-25 and A-155."
FT /evidence="ECO:0000269|PubMed:27080106"
FT MUTAGEN 155
FT /note="K->A: In PBC; loss of inositol polyphosphate
FT binding; when associated with F-25 and A-29."
FT /evidence="ECO:0000269|PubMed:27080106"
FT CONFLICT 125
FT /note="R -> C (in Ref. 6; AK066364)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 320 AA; 35772 MW; 54322E4F03CF1610 CRC64;
MKFGKDFRSH LEETLPAWRD KYLAYKSLKK LIKNLPPDGD PPPVAAAAEV PAGDGDGDGG
IALGNWFARV LDMELQKLND FYIEREEWYV IRLQVLKERI ERVKAKKNGA FTSKSEFTEE
MLEIRKAFVI IHGEMILLQT YSSLNFAGLV KILKKYDKRT GGLLSLPFTQ RARHQPFFTT
EPLTRLVREC EANLELLFPI EAEVLESASS SAKLQPQNDD AASHDPASSV DVETSDVYRS
TLAAMKAIQG LRKASSTYNP LSLARFFHGE DGEACSGAIT SESDSYSDSQ IEDAEDDDKE
VQSREQNTAQ NAAEGQPRDE
