IRO2_ORYSJ
ID IRO2_ORYSJ Reviewed; 247 AA.
AC Q0JFZ0; A9JX09; Q941Z7;
DT 25-OCT-2017, integrated into UniProtKB/Swiss-Prot.
DT 03-OCT-2006, sequence version 1.
DT 03-AUG-2022, entry version 99.
DE RecName: Full=Protein IRON-RELATED TRANSCRIPTION FACTOR 2 {ECO:0000303|PubMed:16887895};
DE Short=OsIRO2 {ECO:0000303|PubMed:16887895};
DE AltName: Full=Basic helix-loop-helix protein 56 {ECO:0000303|PubMed:16896230};
DE Short=OsbHLH056 {ECO:0000303|PubMed:16896230};
GN Name=IRO2 {ECO:0000303|PubMed:16887895};
GN Synonyms=BHLH056 {ECO:0000303|PubMed:16896230};
GN OrderedLocusNames=LOC_Os01g72370 {ECO:0000305}, Os01g0952800 {ECO:0000305};
GN ORFNames=OsJ_04787 {ECO:0000312|EMBL:EAZ14859.1},
GN P0431G06.13-1 {ECO:0000312|EMBL:BAB64701.1};
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 [MRNA], FUNCTION, INDUCTION BY IRON DEFICIENCY, AND
RP TISSUE SPECIFICITY.
RC STRAIN=cv. Nipponbare;
RX PubMed=16887895; DOI=10.1093/jxb/erl054;
RA Ogo Y., Itai R.N., Nakanishi H., Inoue H., Kobayashi T., Suzuki M.,
RA Takahashi M., Mori S., Nishizawa N.K.;
RT "Isolation and characterization of IRO2, a novel iron-regulated bHLH
RT transcription factor in graminaceous plants.";
RL J. Exp. Bot. 57:2867-2878(2006).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12447438; DOI=10.1038/nature01184;
RA Sasaki T., Matsumoto T., Yamamoto K., Sakata K., Baba T., Katayose Y.,
RA Wu J., Niimura Y., Cheng Z., Nagamura Y., Antonio B.A., Kanamori H.,
RA Hosokawa S., Masukawa M., Arikawa K., Chiden Y., Hayashi M., Okamoto M.,
RA Ando T., Aoki H., Arita K., Hamada M., Harada C., Hijishita S., Honda M.,
RA Ichikawa Y., Idonuma A., Iijima M., Ikeda M., Ikeno M., Ito S., Ito T.,
RA Ito Y., Ito Y., Iwabuchi A., Kamiya K., Karasawa W., Katagiri S.,
RA Kikuta A., Kobayashi N., Kono I., Machita K., Maehara T., Mizuno H.,
RA Mizubayashi T., Mukai Y., Nagasaki H., Nakashima M., Nakama Y.,
RA Nakamichi Y., Nakamura M., Namiki N., Negishi M., Ohta I., Ono N., Saji S.,
RA Sakai K., Shibata M., Shimokawa T., Shomura A., Song J., Takazaki Y.,
RA Terasawa K., Tsuji K., Waki K., Yamagata H., Yamane H., Yoshiki S.,
RA Yoshihara R., Yukawa K., Zhong H., Iwama H., Endo T., Ito H., Hahn J.H.,
RA Kim H.-I., Eun M.-Y., Yano M., Jiang J., Gojobori T.;
RT "The genome sequence and structure of rice chromosome 1.";
RL Nature 420:312-316(2002).
RN [3]
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 [4]
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 [5]
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 [6]
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 [7]
RP GENE FAMILY, AND NOMENCLATURE.
RX PubMed=16896230; DOI=10.1104/pp.106.080580;
RA Li X., Duan X., Jiang H., Sun Y., Tang Y., Yuan Z., Guo J., Liang W.,
RA Chen L., Yin J., Ma H., Wang J., Zhang D.;
RT "Genome-wide analysis of basic/helix-loop-helix transcription factor family
RT in rice and Arabidopsis.";
RL Plant Physiol. 141:1167-1184(2006).
RN [8]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. Tsuki-no-hikari;
RX PubMed=17559517; DOI=10.1111/j.1365-313x.2007.03149.x;
RA Ogo Y., Itai R.N., Nakanishi H., Kobayashi T., Takahashi M., Mori S.,
RA Nishizawa N.K.;
RT "The rice bHLH protein OsIRO2 is an essential regulator of the genes
RT involved in Fe uptake under Fe-deficient conditions.";
RL Plant J. 51:366-377(2007).
RN [9]
RP INDUCTION BY IRON DEFICIENCY.
RC STRAIN=cv. Nipponbare;
RX PubMed=18025467; DOI=10.1073/pnas.0707010104;
RA Kobayashi T., Ogo Y., Nakanishi Itai R., Nakanishi H., Takahashi M.,
RA Mori S., Nishizawa N.K.;
RT "The transcription factor IDEF1 regulates the response to and tolerance of
RT iron deficiency in plants.";
RL Proc. Natl. Acad. Sci. U.S.A. 104:19150-19155(2007).
RN [10]
RP INDUCTION BY IRON DEFICIENCY.
RC STRAIN=cv. Tsuki-no-hikari;
RX PubMed=19737364; DOI=10.1111/j.1365-313x.2009.04015.x;
RA Kobayashi T., Itai R.N., Ogo Y., Kakei Y., Nakanishi H., Takahashi M.,
RA Nishizawa N.K.;
RT "The rice transcription factor IDEF1 is essential for the early response to
RT iron deficiency, and induces vegetative expression of late embryogenesis
RT abundant genes.";
RL Plant J. 60:948-961(2009).
RN [11]
RP FUNCTION, DISRUPTION PHENOTYPE, AND INDUCTION BY IRON DEFICIENCY AND
RP ETHYLENE.
RC STRAIN=cv. Nipponbare;
RX PubMed=21112958; DOI=10.1093/jxb/erq301;
RA Wu J., Wang C., Zheng L., Wang L., Chen Y., Whelan J., Shou H.;
RT "Ethylene is involved in the regulation of iron homeostasis by regulating
RT the expression of iron-acquisition-related genes in Oryza sativa.";
RL J. Exp. Bot. 62:667-674(2011).
RN [12]
RP FUNCTION, DISRUPTION PHENOTYPE, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE,
RP AND INDUCTION BY IRON DEFICIENCY.
RC STRAIN=cv. Nipponbare;
RX PubMed=21331630; DOI=10.1007/s11103-011-9752-6;
RA Ogo Y., Itai R.N., Kobayashi T., Aung M.S., Nakanishi H., Nishizawa N.K.;
RT "OsIRO2 is responsible for iron utilization in rice and improves growth and
RT yield in calcareous soil.";
RL Plant Mol. Biol. 75:593-605(2011).
RN [13]
RP INDUCTION BY IRON DEFICIENCY.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280375; DOI=10.1186/1939-8433-6-16;
RA Itai R.N., Ogo Y., Kobayashi T., Nakanishi H., Nishizawa N.K.;
RT "Rice genes involved in phytosiderophore biosynthesis are synchronously
RT regulated during the early stages of iron deficiency in roots.";
RL Rice 6:16-16(2013).
RN [14]
RP REVIEW.
RX PubMed=24351075; DOI=10.1186/1939-8433-6-40;
RA Masuda H., Aung M.S., Nishizawa N.K.;
RT "Iron biofortification of rice using different transgenic approaches.";
RL Rice 6:40-40(2013).
RN [15]
RP FUNCTION, INDUCTION BY IRON DEFICIENCY, AND REVIEW.
RX PubMed=26224556; DOI=10.1186/s12284-014-0027-0;
RA Kobayashi T., Nakanishi Itai R., Nishizawa N.K.;
RT "Iron deficiency responses in rice roots.";
RL Rice 7:27-27(2014).
RN [16]
RP INDUCTION BY NITRIC OXIDE AND ARSENATE.
RX PubMed=26793232; DOI=10.3389/fpls.2015.01272;
RA Singh A.P., Dixit G., Kumar A., Mishra S., Singh P.K., Dwivedi S.,
RA Trivedi P.K., Chakrabarty D., Mallick S., Pandey V., Dhankher O.P.,
RA Tripathi R.D.;
RT "Nitric oxide alleviated arsenic toxicity by modulation of antioxidants and
RT thiol metabolism in rice (Oryza sativa L.).";
RL Front. Plant Sci. 6:1272-1272(2015).
RN [17]
RP INDUCTION BY CADMIUM.
RX PubMed=27412910; DOI=10.1111/pce.12793;
RA Feng S.J., Liu X.S., Tao H., Tan S.K., Chu S.S., Oono Y., Zhang X.D.,
RA Chen J., Yang Z.M.;
RT "Variation of DNA methylation patterns associated with gene expression in
RT rice (Oryza sativa) exposed to cadmium.";
RL Plant Cell Environ. 39:2629-2649(2016).
RN [18]
RP HOMODIMERIZATION, INTERACTION WITH BHLH156, AND SUBCELLULAR LOCATION.
RX PubMed=31574173; DOI=10.1111/nph.16232;
RA Wang S., Li L., Ying Y., Wang J., Shao J.F., Yamaji N., Whelan J., Ma J.F.,
RA Shou H.;
RT "A transcription factor OsbHLH156 regulates Strategy II iron acquisition
RT through localizing IRO2 to the nucleus in rice.";
RL New Phytol. 225:1247-1260(2020).
CC -!- FUNCTION: Transcription activator that binds to the DNA motif 5'-
CC CACGTGG-3' in the promoter of iron (Fe) deficiency-inducible genes as
CC well as of genes involved in iron homeostasis, thus contributing to
CC basal tolerance to iron deficiency, iron uptake from soil and iron
CC transport, particularly during seed maturation and germination
CC (PubMed:16887895, PubMed:17559517, PubMed:21331630, PubMed:26224556).
CC Promotes the accumulation of mugineic acid family phytosiderophores
CC (MAs) (PubMed:17559517). Required for ethylene-mediated signaling
CC during iron deficiency responses (PubMed:21112958). Improves growth and
CC yield, especially in calcareous soil with low iron availability.
CC Promotes iron concentration in shoots and grain (PubMed:21331630).
CC {ECO:0000269|PubMed:16887895, ECO:0000269|PubMed:17559517,
CC ECO:0000269|PubMed:21112958, ECO:0000269|PubMed:21331630,
CC ECO:0000269|PubMed:26224556}.
CC -!- SUBUNIT: Forms homodimers (PubMed:31574173). Interacts with BHLH156 in
CC the nucleus (PubMed:31574173). {ECO:0000269|PubMed:31574173}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00768,
CC ECO:0000255|PROSITE-ProRule:PRU00981, ECO:0000269|PubMed:31574173}.
CC Cytoplasm {ECO:0000269|PubMed:31574173}. Note=Localized partially to
CC the nucleus under iron deficiency conditions.
CC {ECO:0000269|PubMed:31574173}.
CC -!- TISSUE SPECIFICITY: Expressed constitutively at low levels in the roots
CC (PubMed:16887895, PubMed:21331630). Also observed in flowers,
CC developing seeds, embryos and vascular bundles (PubMed:21331630).
CC {ECO:0000269|PubMed:16887895, ECO:0000269|PubMed:21331630}.
CC -!- DEVELOPMENTAL STAGE: During seeds germination, detected in embryos. In
CC vegetative tissues under iron-sufficient, restricted almost exclusively
CC to vascular bundles of roots and leaves, and to the root exodermis. In
CC response to iron deficiency, accumulates in all tissues of roots and
CC leaves. {ECO:0000269|PubMed:21331630}.
CC -!- INDUCTION: Strongly induced in both roots and shoots during iron (Fe)
CC deficiency stress (PubMed:16887895, PubMed:18025467, PubMed:19737364,
CC PubMed:21112958, PubMed:21331630, PubMed:24280375). Ethylene enhances
CC the iron deficiency-mediated induction (PubMed:21112958). Induced by
CC arsenate (AsV25 and AsV50); this induction is repressed by nitric oxide
CC (NO) (PubMed:26793232). Accumulates under cadmium (Cd) stress; this
CC induction is inhibited by the DNA methyltransferase inhibitor 5-aza-2-
CC deoxycytidine (Aza) (PubMed:27412910). {ECO:0000269|PubMed:16887895,
CC ECO:0000269|PubMed:18025467, ECO:0000269|PubMed:19737364,
CC ECO:0000269|PubMed:21112958, ECO:0000269|PubMed:21331630,
CC ECO:0000269|PubMed:24280375, ECO:0000269|PubMed:26793232,
CC ECO:0000269|PubMed:27412910}.
CC -!- DISRUPTION PHENOTYPE: Reduced growth compared after germination
CC (PubMed:21331630). Lower mugineic acid family phytosiderophores (MAs)
CC secretion and hypersensitivity to iron (Fe) deficiency
CC (PubMed:17559517). Reduced induction of genes involved in iron
CC homeostasis upon iron deficiency and ethylene treatment
CC (PubMed:21112958). {ECO:0000269|PubMed:17559517,
CC ECO:0000269|PubMed:21112958, ECO:0000269|PubMed:21331630}.
CC -!- SIMILARITY: Belongs to the bHLH protein family. {ECO:0000305}.
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DR EMBL; BR000688; FAA00382.1; -; mRNA.
DR EMBL; AP003683; BAB64701.1; -; Genomic_DNA.
DR EMBL; AP008207; BAF07338.1; -; Genomic_DNA.
DR EMBL; AP014957; BAS76260.1; -; Genomic_DNA.
DR EMBL; CM000138; EAZ14859.1; -; Genomic_DNA.
DR RefSeq; XP_015612709.1; XM_015757223.1.
DR AlphaFoldDB; Q0JFZ0; -.
DR SMR; Q0JFZ0; -.
DR STRING; 4530.OS01T0952800-01; -.
DR PaxDb; Q0JFZ0; -.
DR PRIDE; Q0JFZ0; -.
DR EnsemblPlants; Os01t0952800-01; Os01t0952800-01; Os01g0952800.
DR GeneID; 4325750; -.
DR Gramene; Os01t0952800-01; Os01t0952800-01; Os01g0952800.
DR KEGG; osa:4325750; -.
DR eggNOG; ENOG502RXMR; Eukaryota.
DR HOGENOM; CLU_089779_0_0_1; -.
DR InParanoid; Q0JFZ0; -.
DR OMA; AIQISMR; -.
DR OrthoDB; 1275266at2759; -.
DR Proteomes; UP000000763; Chromosome 1.
DR Proteomes; UP000007752; Chromosome 1.
DR Proteomes; UP000059680; Chromosome 1.
DR ExpressionAtlas; Q0JFZ0; baseline and differential.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0090575; C:RNA polymerase II transcription regulator complex; IBA:GO_Central.
DR GO; GO:0003700; F:DNA-binding transcription factor activity; IDA:UniProtKB.
DR GO; GO:0000981; F:DNA-binding transcription factor activity, RNA polymerase II-specific; IBA:GO_Central.
DR GO; GO:0046983; F:protein dimerization activity; IEA:InterPro.
DR GO; GO:0000977; F:RNA polymerase II transcription regulatory region sequence-specific DNA binding; IBA:GO_Central.
DR GO; GO:0009873; P:ethylene-activated signaling pathway; IEA:UniProtKB-KW.
DR GO; GO:1900706; P:positive regulation of siderophore biosynthetic process; IMP:UniProtKB.
DR GO; GO:0045893; P:positive regulation of transcription, DNA-templated; IDA:UniProtKB.
DR GO; GO:0010104; P:regulation of ethylene-activated signaling pathway; IMP:UniProtKB.
DR GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR GO; GO:0006355; P:regulation of transcription, DNA-templated; IDA:UniProtKB.
DR GO; GO:0046685; P:response to arsenic-containing substance; IEP:UniProtKB.
DR GO; GO:0046686; P:response to cadmium ion; IEP:UniProtKB.
DR GO; GO:0009723; P:response to ethylene; IEP:UniProtKB.
DR GO; GO:1990641; P:response to iron ion starvation; IMP:UniProtKB.
DR GO; GO:0071731; P:response to nitric oxide; IEP:UniProtKB.
DR Gene3D; 4.10.280.10; -; 1.
DR InterPro; IPR011598; bHLH_dom.
DR InterPro; IPR036638; HLH_DNA-bd_sf.
DR InterPro; IPR015660; MASH1/Ascl1a-like.
DR PANTHER; PTHR13935; PTHR13935; 1.
DR Pfam; PF00010; HLH; 1.
DR SMART; SM00353; HLH; 1.
DR SUPFAM; SSF47459; SSF47459; 1.
DR PROSITE; PS50888; BHLH; 1.
PE 1: Evidence at protein level;
KW Activator; Cytoplasm; DNA-binding; Ethylene signaling pathway; Iron;
KW Nucleus; Reference proteome; Stress response; Transcription;
KW Transcription regulation.
FT CHAIN 1..247
FT /note="Protein IRON-RELATED TRANSCRIPTION FACTOR 2"
FT /id="PRO_0000442063"
FT DOMAIN 68..119
FT /note="bHLH"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00981"
FT REGION 68..81
FT /note="Basic motif"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00981"
FT REGION 82..119
FT /note="Helix-loop-helix motif"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00981"
FT MOTIF 68..75
FT /note="Nuclear localization signal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00768"
FT CONFLICT 86
FT /note="E -> K (in Ref. 1; FAA00382)"
FT /evidence="ECO:0000305"
FT CONFLICT 95
FT /note="L -> I (in Ref. 1; FAA00382)"
FT /evidence="ECO:0000305"
FT CONFLICT 101
FT /note="T -> TK (in Ref. 2; BAB64701 and 6; EAZ14859)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 247 AA; 26962 MW; 1BDDDBADCC236C2B CRC64;
MEQLFVDDPA FASSMSSLEA DIFSGAGQLP SSPWLDLDLD DDVQDLSMAP TTANAVSSGY
GSGGSGSHRK LSHNAYERDR RKQLNELYSS LRALLPDADH TKLSIPTTVS RVLKYIPELQ
KQVENLERKK KELTTTSTTN CKPGVLGSQL MSEGMAPIVS ATCINDMEIM VQVSLLSNVA
GSVLPLSKCI KVLENEGLHF ISSSTSSGFG NRTFYSIHLQ RSEGTINEEC PAFCERLEKV
VRNKAKL
