NINJA_ARATH
ID NINJA_ARATH Reviewed; 425 AA.
AC Q9SV55; Q940F7;
DT 14-APR-2009, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 115.
DE RecName: Full=AFP homolog 2 {ECO:0000303|PubMed:18484180};
DE AltName: Full=Novel interactor of JAZ {ECO:0000303|PubMed:20360743};
GN Name=AFPH2 {ECO:0000303|PubMed:18484180};
GN Synonyms=NINJA {ECO:0000303|PubMed:20360743};
GN OrderedLocusNames=At4g28910 {ECO:0000312|Araport:AT4G28910};
GN ORFNames=F25O24.30 {ECO:0000312|EMBL:CAB43905.1};
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=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 NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=19423640; DOI=10.1093/dnares/dsp009;
RA Iida K., Fukami-Kobayashi K., Toyoda A., Sakaki Y., Kobayashi M., Seki M.,
RA Shinozaki K.;
RT "Analysis of multiple occurrences of alternative splicing events in
RT Arabidopsis thaliana using novel sequenced full-length cDNAs.";
RL DNA Res. 16:155-164(2009).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RA Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA Feldmann K.A.;
RT "Full-length cDNA from Arabidopsis thaliana.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP GENE FAMILY, AND NOMENCLATURE.
RX PubMed=18484180; DOI=10.1007/s11103-008-9344-2;
RA Garcia M.E., Lynch T.J., Peeters J., Snowden C., Finkelstein R.R.;
RT "A small plant-specific protein family of ABI five binding proteins (AFPs)
RT regulates stress response in germinating Arabidopsis seeds and seedlings.";
RL Plant Mol. Biol. 67:643-658(2008).
RN [7]
RP FUNCTION, INTERACTION WITH TIFY10A/JAZ1; TIFY10B/JAZ2; TIFY6B/JAZ3;
RP TIFY6A/JAZ4; TIFY11A/JAZ5; TIFY11B/JAZ6; TIFY7/JAZ9; TIFY9/JAZ10;
RP TIFY3A/JAZ11; TIFY3B/JAZ12; TIFY4A/PPD1; TIFY4B/PPD2; TIFY8 AND TOPLESS,
RP INDUCTION BY JASMONATE, SUBCELLULAR LOCATION, AND MUTAGENESIS OF LEU-9;
RP LEU-11 AND LEU-13.
RX PubMed=20360743; DOI=10.1038/nature08854;
RA Pauwels L., Barbero G.F., Geerinck J., Tilleman S., Grunewald W.,
RA Perez A.C., Chico J.M., Bossche R.V., Sewell J., Gil E., Garcia-Casado G.,
RA Witters E., Inze D., Long J.A., De Jaeger G., Solano R., Goossens A.;
RT "NINJA connects the co-repressor TOPLESS to jasmonate signalling.";
RL Nature 464:788-791(2010).
RN [8]
RP FUNCTION.
RX PubMed=24003128; DOI=10.1073/pnas.1307910110;
RA Acosta I.F., Gasperini D., Chetelat A., Stolz S., Santuari L., Farmer E.E.;
RT "Role of NINJA in root jasmonate signaling.";
RL Proc. Natl. Acad. Sci. U.S.A. 110:15473-15478(2013).
RN [9]
RP FUNCTION, AND INTERACTION WITH TOPLESS AND TIFY8.
RX PubMed=24416306; DOI=10.1371/journal.pone.0084891;
RA Cuellar Perez A., Nagels Durand A., Vanden Bossche R., De Clercq R.,
RA Persiau G., Van Wees S.C., Pieterse C.M., Gevaert K., De Jaeger G.,
RA Goossens A., Pauwels L.;
RT "The non-JAZ TIFY protein TIFY8 from Arabidopsis thaliana is a
RT transcriptional repressor.";
RL PLoS ONE 9:E84891-E84891(2014).
RN [10]
RP INTERACTION WITH PAT1H1.
RX PubMed=26956135; DOI=10.1007/s00299-016-1961-7;
RA Yu Q., Liu J., Zheng H., Jia Y., Tian H., Ding Z.;
RT "Topoisomerase II-associated protein PAT1H1 is involved in the root stem
RT cell niche maintenance in Arabidopsis thaliana.";
RL Plant Cell Rep. 35:1297-1307(2016).
RN [11]
RP X-RAY CRYSTALLOGRAPHY (3.10 ANGSTROMS) OF 4-14 IN COMPLEX WITH RICE TPR1.
RX PubMed=26601214; DOI=10.1126/sciadv.1500107;
RA Ke J., Ma H., Gu X., Thelen A., Brunzelle J.S., Li J., Xu H.E., Melcher K.;
RT "Structural basis for recognition of diverse transcriptional repressors by
RT the TOPLESS family of corepressors.";
RL Sci. Adv. 1:E1500107-E1500107(2015).
CC -!- FUNCTION: Acts as a transcriptional repressor. Negative regulator of
CC jasmonate responses. Connects the JAZ proteins and the non-JAZ protein
CC TIFY8 with the TOPLESS corepressors. {ECO:0000269|PubMed:20360743,
CC ECO:0000269|PubMed:24003128, ECO:0000269|PubMed:24416306}.
CC -!- SUBUNIT: Component of a complex at least composed of TOPLESS, TPR2,
CC TPR3, TIFY4B/PPD2, MYC3/ATR2 and TIFY3B/JAZ12. Interacts (via C-
CC terminus) with TIFY10A/JAZ1; TIFY10B/JAZ2; TIFY6B/JAZ3; TIFY6A/JAZ4;
CC TIFY11A/JAZ5; TIFY11B/JAZ6; TIFY7/JAZ9; TIFY9/JAZ10; TIFY3A/JAZ11;
CC TIFY3B/JAZ12; TIFY4A/PPD1; TIFY4B/PPD2 and TIFY8 (via TIFY domain).
CC Interacts with TOPLESS (PubMed:20360743, PubMed:24416306). Interacts
CC with PAT1H1 (PubMed:26956135). {ECO:0000269|PubMed:20360743,
CC ECO:0000269|PubMed:24416306, ECO:0000269|PubMed:26956135}.
CC -!- INTERACTION:
CC Q9SV55; Q9MAA7: GID1A; NbExp=3; IntAct=EBI-1787005, EBI-963597;
CC Q9SV55; Q9LMA8: TIFY10A; NbExp=9; IntAct=EBI-1787005, EBI-1388539;
CC Q9SV55; Q9S7M2: TIFY10B; NbExp=6; IntAct=EBI-1787005, EBI-1792563;
CC Q9SV55; Q9LDU5: TIFY11A; NbExp=10; IntAct=EBI-1787005, EBI-2312095;
CC Q9SV55; Q9C9E3: TIFY11B; NbExp=9; IntAct=EBI-1787005, EBI-2312120;
CC Q9SV55; Q9C5K8: TIFY3B; NbExp=7; IntAct=EBI-1787005, EBI-2312231;
CC Q9SV55; Q8GY55: TIFY4B; NbExp=7; IntAct=EBI-1787005, EBI-15206004;
CC Q9SV55; Q58G47: TIFY6A; NbExp=2; IntAct=EBI-1787005, EBI-2312053;
CC Q9SV55; Q9LVI4: TIFY6B; NbExp=3; IntAct=EBI-1787005, EBI-1792431;
CC Q9SV55; Q8W4J8: TIFY7; NbExp=9; IntAct=EBI-1787005, EBI-1792583;
CC Q9SV55; Q84MB2: TIFY8; NbExp=6; IntAct=EBI-1787005, EBI-4426557;
CC Q9SV55; Q93ZM9: TIFY9; NbExp=7; IntAct=EBI-1787005, EBI-2312172;
CC Q9SV55; Q94AI7: TPL; NbExp=4; IntAct=EBI-1787005, EBI-2119299;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:20360743}.
CC -!- INDUCTION: By jasmonate. {ECO:0000269|PubMed:20360743}.
CC -!- MISCELLANEOUS: Unlike the JAZ proteins, the stability of AFPH2/NINJA is
CC unaffected by jasmonate.
CC -!- SIMILARITY: Belongs to the Ninja family. {ECO:0000305}.
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DR EMBL; AL078469; CAB43905.1; -; Genomic_DNA.
DR EMBL; AL161573; CAB81479.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE85560.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE85561.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE85562.1; -; Genomic_DNA.
DR EMBL; AY054672; AAK96863.1; -; mRNA.
DR EMBL; AY065350; AAL38791.1; -; mRNA.
DR EMBL; AY096726; AAM20360.1; -; mRNA.
DR EMBL; AK316690; BAH19417.1; -; mRNA.
DR EMBL; AY085087; AAM61641.1; -; mRNA.
DR PIR; T08946; T08946.
DR RefSeq; NP_001078466.1; NM_001084997.1.
DR RefSeq; NP_194620.1; NM_119035.3.
DR RefSeq; NP_849467.1; NM_179136.3.
DR PDB; 5C6V; X-ray; 3.10 A; E/F/G/H=4-14.
DR PDBsum; 5C6V; -.
DR AlphaFoldDB; Q9SV55; -.
DR SMR; Q9SV55; -.
DR BioGRID; 14299; 79.
DR DIP; DIP-40581N; -.
DR IntAct; Q9SV55; 21.
DR STRING; 3702.AT4G28910.2; -.
DR iPTMnet; Q9SV55; -.
DR PaxDb; Q9SV55; -.
DR PRIDE; Q9SV55; -.
DR ProteomicsDB; 249437; -.
DR EnsemblPlants; AT4G28910.1; AT4G28910.1; AT4G28910.
DR EnsemblPlants; AT4G28910.2; AT4G28910.2; AT4G28910.
DR EnsemblPlants; AT4G28910.3; AT4G28910.3; AT4G28910.
DR GeneID; 829012; -.
DR Gramene; AT4G28910.1; AT4G28910.1; AT4G28910.
DR Gramene; AT4G28910.2; AT4G28910.2; AT4G28910.
DR Gramene; AT4G28910.3; AT4G28910.3; AT4G28910.
DR KEGG; ath:AT4G28910; -.
DR Araport; AT4G28910; -.
DR TAIR; locus:2123573; AT4G28910.
DR eggNOG; ENOG502QSTR; Eukaryota.
DR HOGENOM; CLU_049096_0_0_1; -.
DR InParanoid; Q9SV55; -.
DR OMA; PMLDKDN; -.
DR OrthoDB; 641759at2759; -.
DR PhylomeDB; Q9SV55; -.
DR PRO; PR:Q9SV55; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q9SV55; baseline and differential.
DR Genevisible; Q9SV55; AT.
DR GO; GO:0005634; C:nucleus; IDA:TAIR.
DR GO; GO:0006952; P:defense response; IEA:UniProtKB-KW.
DR GO; GO:0009867; P:jasmonic acid mediated signaling pathway; IMP:TAIR.
DR GO; GO:0045892; P:negative regulation of transcription, DNA-templated; IDA:TAIR.
DR GO; GO:1901371; P:regulation of leaf morphogenesis; IMP:TAIR.
DR GO; GO:0009753; P:response to jasmonic acid; IEP:TAIR.
DR InterPro; IPR031307; Ninja_fam.
DR InterPro; IPR032308; TDBD.
DR PANTHER; PTHR31413; PTHR31413; 1.
DR Pfam; PF16135; TDBD; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Jasmonic acid signaling pathway; Nucleus; Plant defense;
KW Reference proteome; Repressor; Transcription; Transcription regulation.
FT CHAIN 1..425
FT /note="AFP homolog 2"
FT /id="PRO_0000369618"
FT REGION 1..207
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 7..17
FT /note="Necessary and sufficient for the interaction with
FT TOPLESS"
FT REGION 288..327
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 322..425
FT /note="Necessary and sufficient for the interaction with
FT the JAZ proteins"
FT COMPBIAS 19..39
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 60..95
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 100..148
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 167..207
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MUTAGEN 9
FT /note="L->A: Loss of interaction with TOPLESS, but no
FT effect on the interaction with TIFY10A/JAZ1; when
FT associated with A-11 and A-13."
FT /evidence="ECO:0000269|PubMed:20360743"
FT MUTAGEN 11
FT /note="L->A: Loss of interaction with TOPLESS, but no
FT effect on the interaction with TIFY10A/JAZ1; when
FT associated with A-9 and A-13."
FT /evidence="ECO:0000269|PubMed:20360743"
FT MUTAGEN 13
FT /note="L->A: Loss of interaction with TOPLESS, but no
FT effect on the interaction with TIFY10A/JAZ1; when
FT associated with A-9 and A-11."
FT /evidence="ECO:0000269|PubMed:20360743"
FT CONFLICT 106
FT /note="D -> E (in Ref. 3; AAK96863)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 425 AA; 44938 MW; 1796FB2FAAB0FB89 CRC64;
MDDDNGLELS LGLSCGGSTG KAKGNNNNNA GSSSENYRAE GGDRSAKVID DFKNFLHPTS
QRPAEPSSGS QRSDSGQQPP QNFFNDLSKA PTTEAEASTK PLWVEDESRK EAGNKRKFGF
PGMNDDKKKE KDSSHVDMHE KKTKASHVST ATDEGSTAEN EDVAESEVGG GSSSNHAKEV
VRPPTDTNIV DNLTGQRRSN HGGSGTEEFT MRNMSYTVPF TVHPQNVVTS MPYSLPTKES
GQHAAATSLL QPNANAGNLP IMFGYSPVQL PMLDKDGSGG IVALSQSPFA GRVPSNSATA
KGEGKQPVAE EGSSEDASER PTGDNSNLNT AFSFDFSAIK PGMAADVKFG GSGARPNLPW
VSTTGSGPHG RTISGVTYRY NANQIKIVCA CHGSHMSPEE FVRHASEEYV SPESSMGMTA
ASAHT
