TDR_ORYSJ
ID TDR_ORYSJ Reviewed; 552 AA.
AC Q6YUS3;
DT 08-JUN-2016, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 03-AUG-2022, entry version 134.
DE RecName: Full=Transcription factor TDR {ECO:0000305};
DE AltName: Full=Basic helix-loop-helix protein 5 {ECO:0000305};
DE Short=OsbHLH005 {ECO:0000303|PubMed:16896230};
DE AltName: Full=Protein TAPETUM DEGENERATION RETARDATION {ECO:0000303|PubMed:17138695};
GN Name=TDR {ECO:0000303|PubMed:17138695}; Synonyms=BHLH5 {ECO:0000305};
GN OrderedLocusNames=Os02g0120500 {ECO:0000312|EMBL:BAF07624.1},
GN LOC_Os02g02820 {ECO:0000305};
GN ORFNames=OJ1020_C02.6 {ECO:0000312|EMBL:BAD07594.1},
GN OsJ_05158 {ECO:0000312|EMBL:EEE56199.1},
GN OSJNBb0088N06.15 {ECO:0000312|EMBL:BAD08134.1};
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 [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 [2]
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 [3]
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 [4]
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 [5]
RP FUNCTION, SUBCELLULAR LOCATION, AND DISRUPTION PHENOTYPE.
RX PubMed=17138695; DOI=10.1105/tpc.106.044107;
RA Li N., Zhang D.S., Liu H.S., Yin C.S., Li X.X., Liang W.Q., Yuan Z., Xu B.,
RA Chu H.W., Wang J., Wen T.Q., Huang H., Luo D., Ma H., Zhang D.B.;
RT "The rice tapetum degeneration retardation gene is required for tapetum
RT degradation and anther development.";
RL Plant Cell 18:2999-3014(2006).
RN [6]
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 [7]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=19825565; DOI=10.1093/mp/ssn028;
RA Zhang D.S., Liang W.Q., Yuan Z., Li N., Shi J., Wang J., Liu Y.M., Yu W.J.,
RA Zhang D.B.;
RT "Tapetum degeneration retardation is critical for aliphatic metabolism and
RT gene regulation during rice pollen development.";
RL Mol. Plant 1:599-610(2008).
RN [8]
RP SUBUNIT, INTERACTION WITH EAT1/DTD, AND SUBCELLULAR LOCATION.
RX PubMed=23519457; DOI=10.1093/mp/sst046;
RA Ji C., Li H., Chen L., Xie M., Wang F., Chen Y., Liu Y.G.;
RT "A novel rice bHLH transcription factor, DTD, acts coordinately with TDR in
RT controlling tapetum function and pollen development.";
RL Mol. Plant 6:1715-1718(2013).
RN [9]
RP FUNCTION, INTERACTION WITH EAT1/DTD, AND SUBCELLULAR LOCATION.
RX PubMed=23385589; DOI=10.1038/ncomms2396;
RA Niu N., Liang W., Yang X., Jin W., Wilson Z.A., Hu J., Zhang D.;
RT "EAT1 promotes tapetal cell death by regulating aspartic proteases during
RT male reproductive development in rice.";
RL Nat. Commun. 4:1445-1445(2013).
RN [10]
RP INTERACTION WITH TIP2.
RX PubMed=24894043; DOI=10.1105/tpc.114.126292;
RA Ko S.S., Li M.J., Sun-Ben Ku M., Ho Y.C., Lin Y.J., Chuang M.H.,
RA Hsing H.X., Lien Y.C., Yang H.T., Chang H.C., Chan M.T.;
RT "The bHLH142 transcription factor coordinates with TDR1 to modulate the
RT expression of EAT1 and regulate pollen development in rice.";
RL Plant Cell 26:2486-2504(2014).
CC -!- FUNCTION: Transcription factor involved in the regulation of tapetum
CC programmed cell death (PCD) and degradation during male reproductive
CC development. Promotes tapetal PCD. Positively regulates the expression
CC of two tapetum-specific genes, the cysteine protease CP1 and the lipid-
CC transfer protein C6 (PubMed:17138695). Acts upstream from and interacts
CC with EAT1/DTD in the regulation of tapetal PCD (PubMed:23385589).
CC Regulates the expression of genes related to aliphatic metabolism
CC during pollen development. May play regulatory role in the lipidic
CC metabolism involved in the formation of pollen wall (PubMed:19825565).
CC {ECO:0000269|PubMed:17138695, ECO:0000269|PubMed:19825565,
CC ECO:0000269|PubMed:23385589}.
CC -!- SUBUNIT: Homodimer (PubMed:23519457). Interacts with EAT1/DTD
CC (PubMed:23519457, PubMed:23385589). Interacts with TIP2
CC (PubMed:24894043). {ECO:0000269|PubMed:23385589,
CC ECO:0000269|PubMed:23519457, ECO:0000269|PubMed:24894043}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00981,
CC ECO:0000269|PubMed:17138695, ECO:0000269|PubMed:23519457}.
CC -!- DISRUPTION PHENOTYPE: Male sterility due to failure of tapetum
CC programmed cell death (PCD) and degeneration, and collapse of
CC microspores in developing anthers (PubMed:17138695). Altered pollen
CC wall formation (PubMed:19825565). {ECO:0000269|PubMed:17138695,
CC ECO:0000269|PubMed:19825565}.
CC -!- SIMILARITY: Belongs to the bHLH protein family.
CC -!- CAUTION: Contains a degenerate basic motif not likely to bind DNA.
CC {ECO:0000255|PROSITE-ProRule:PRU00981}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AP004078; BAD07594.1; -; Genomic_DNA.
DR EMBL; AP005851; BAD08134.1; -; Genomic_DNA.
DR EMBL; AP008208; BAF07624.1; -; Genomic_DNA.
DR EMBL; AP014958; BAS76702.1; -; Genomic_DNA.
DR EMBL; CM000139; EEE56199.1; -; Genomic_DNA.
DR RefSeq; XP_015625730.1; XM_015770244.1.
DR AlphaFoldDB; Q6YUS3; -.
DR SMR; Q6YUS3; -.
DR STRING; 4530.OS02T0120500-01; -.
DR PaxDb; Q6YUS3; -.
DR PRIDE; Q6YUS3; -.
DR EnsemblPlants; Os02t0120500-01; Os02t0120500-01; Os02g0120500.
DR EnsemblPlants; Os02t0120500-02; Os02t0120500-02; Os02g0120500.
DR GeneID; 4328113; -.
DR Gramene; Os02t0120500-01; Os02t0120500-01; Os02g0120500.
DR Gramene; Os02t0120500-02; Os02t0120500-02; Os02g0120500.
DR KEGG; osa:4328113; -.
DR eggNOG; ENOG502QQUB; Eukaryota.
DR HOGENOM; CLU_037477_0_0_1; -.
DR InParanoid; Q6YUS3; -.
DR OMA; NEFFIKV; -.
DR OrthoDB; 922298at2759; -.
DR PlantReactome; R-OSA-8986768; Anther and pollen development.
DR Proteomes; UP000000763; Chromosome 2.
DR Proteomes; UP000007752; Chromosome 2.
DR Proteomes; UP000059680; Chromosome 2.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0003677; F:DNA binding; IMP:Gramene.
DR GO; GO:0003700; F:DNA-binding transcription factor activity; IBA:GO_Central.
DR GO; GO:0046983; F:protein dimerization activity; IEA:InterPro.
DR GO; GO:0043565; F:sequence-specific DNA binding; IBA:GO_Central.
DR GO; GO:0048653; P:anther development; IMP:Gramene.
DR GO; GO:0048654; P:anther morphogenesis; IMP:Gramene.
DR GO; GO:0048657; P:anther wall tapetum cell differentiation; IMP:Gramene.
DR GO; GO:0006355; P:regulation of transcription, DNA-templated; IBA:GO_Central.
DR Gene3D; 4.10.280.10; -; 1.
DR InterPro; IPR011598; bHLH_dom.
DR InterPro; IPR036638; HLH_DNA-bd_sf.
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 Developmental protein; Nucleus; Reference proteome; Transcription;
KW Transcription regulation.
FT CHAIN 1..552
FT /note="Transcription factor TDR"
FT /id="PRO_0000436457"
FT DOMAIN 281..330
FT /note="bHLH"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00981"
FT REGION 241..289
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 281..294
FT /note="Basic motif; degenerate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00981"
FT REGION 295..330
FT /note="Helix-loop-helix motif"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00981"
FT REGION 347..414
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 258..289
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 369..394
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 552 AA; 58274 MW; B12EA5E1704C2D55 CRC64;
MGRGDHLLMK NSNAAAAAAA VNGGGTSLDA ALRPLVGSDG WDYCIYWRLS PDQRFLEMTG
FCCSSELEAQ VSALLDLPSS IPLDSSSIGM HAQALLSNQP IWQSSSEEEE ADGGGGAKTR
LLVPVAGGLV ELFASRYMAE EQQMAELVMA QCGGGGAGDD GGGQAWPPPE TPSFQWDGGA
DAQRLMYGGS SLNLFDAAAA DDDPFLGGGG GDAVGDEAAA AGAWPYAGMA VSEPSVAVAQ
EQMQHAAGGG VAESGSEGRK LHGGDPEDDG DGEGRSGGAK RQQCKNLEAE RKRRKKLNGH
LYKLRSLVPN ITKMDRASIL GDAIDYIVGL QKQVKELQDE LEDNHVHHKP PDVLIDHPPP
ASLVGLDNDD ASPPNSHQQQ PPLAVSGSSS RRSNKDPAMT DDKVGGGGGG GHRMEPQLEV
RQVQGNELFV QVLWEHKPGG FVRLMDAMNA LGLEVINVNV TTYKTLVLNV FRVMVRDSEV
AVQADRVRDS LLEVTRETYP GVWPSPQEED DAKFDGGDGG QAAAAAAAAG GEHYHDEVGG
GYHQHLHYLA FD
