LHY_ARATH
ID LHY_ARATH Reviewed; 645 AA.
AC Q6R0H1; B9DFD7; B9DFM4; O81713; Q9MAM8;
DT 24-NOV-2009, integrated into UniProtKB/Swiss-Prot.
DT 24-NOV-2009, sequence version 2.
DT 03-AUG-2022, entry version 140.
DE RecName: Full=Protein LHY {ECO:0000303|PubMed:9657154};
DE AltName: Full=MYB-related transcription factor LHY {ECO:0000303|PubMed:9657154};
DE AltName: Full=Protein LATE ELONGATED HYPOCOTYL {ECO:0000303|PubMed:9657154};
GN Name=LHY {ECO:0000303|PubMed:9657154};
GN OrderedLocusNames=At1g01060 {ECO:0000312|Araport:AT1G01060};
GN ORFNames=T25K16.6 {ECO:0000312|EMBL:AAF26474.1};
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 [MRNA], FUNCTION, AND INDUCTION.
RX PubMed=9657154; DOI=10.1016/s0092-8674(00)81465-8;
RA Schaffer R., Ramsay N., Samach A., Corden S., Putterill J., Carre I.A.,
RA Coupland G.;
RT "The late elongated hypocotyl mutation of Arabidopsis disrupts circadian
RT rhythms and the photoperiodic control of flowering.";
RL Cell 93:1219-1229(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA], AND GENE FAMILY.
RX PubMed=16463103; DOI=10.1007/s11103-005-2910-y;
RA Chen Y., Yang X., He K., Liu M., Li J., Gao Z., Lin Z., Zhang Y., Wang X.,
RA Qiu X., Shen Y., Zhang L., Deng X., Luo J., Deng X.-W., Chen Z., Gu H.,
RA Qu L.-J.;
RT "The MYB transcription factor superfamily of Arabidopsis: expression
RT analysis and phylogenetic comparison with the rice MYB family.";
RL Plant Mol. Biol. 60:107-124(2006).
RN [3]
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 [4]
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 [5]
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 [6]
RP PHOSPHORYLATION, AND INTERACTION WITH CKB1 AND CKB3.
RX PubMed=10535927; DOI=10.1073/pnas.96.22.12362;
RA Sugano S., Andronis C., Ong M.S., Green R.M., Tobin E.M.;
RT "The protein kinase CK2 is involved in regulation of circadian rhythms in
RT Arabidopsis.";
RL Proc. Natl. Acad. Sci. U.S.A. 96:12362-12366(1999).
RN [7]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=12015970; DOI=10.1016/s1534-5807(02)00170-3;
RA Mizoguchi T., Wheatley K., Hanzawa Y., Wright L., Mizoguchi M., Song H.-R.,
RA Carre I.A., Coupland G.;
RT "LHY and CCA1 are partially redundant genes required to maintain circadian
RT rhythms in Arabidopsis.";
RL Dev. Cell 2:629-641(2002).
RN [8]
RP INDUCTION BY LIGHT.
RX PubMed=12574129; DOI=10.1093/emboj/cdg075;
RA Kim J.Y., Song H.R., Taylor B.L., Carre I.A.;
RT "Light-regulated translation mediates gated induction of the Arabidopsis
RT clock protein LHY.";
RL EMBO J. 22:935-944(2003).
RN [9]
RP FUNCTION, TISSUE SPECIFICITY, AND INDUCTION.
RX PubMed=19095940; DOI=10.1126/science.1161403;
RA James A.B., Monreal J.A., Nimmo G.A., Kelly C.L., Herzyk P., Jenkins G.I.,
RA Nimmo H.G.;
RT "The circadian clock in Arabidopsis roots is a simplified slave version of
RT the clock in shoots.";
RL Science 322:1832-1835(2008).
RN [10]
RP FUNCTION, INDUCTION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY, SUBUNIT,
RP INTERACTION WITH CCA1, DNA-BINDING, AND DISRUPTION PHENOTYPE.
RX PubMed=19218364; DOI=10.1104/pp.108.133272;
RA Lu S.X., Knowles S.M., Andronis C., Ong M.S., Tobin E.M.;
RT "CIRCADIAN CLOCK ASSOCIATED1 and LATE ELONGATED HYPOCOTYL function
RT synergistically in the circadian clock of Arabidopsis.";
RL Plant Physiol. 150:834-843(2009).
RN [11]
RP INTERACTION WITH CCA1.
RX PubMed=19339503; DOI=10.1104/pp.109.137414;
RA Yakir E., Hilman D., Kron I., Hassidim M., Melamed-Book N., Green R.M.;
RT "Posttranslational regulation of CIRCADIAN CLOCK ASSOCIATED1 in the
RT circadian oscillator of Arabidopsis.";
RL Plant Physiol. 150:844-857(2009).
RN [12]
RP INDUCTION.
RX PubMed=19286557; DOI=10.1126/science.1167206;
RA Pruneda-Paz J.L., Breton G., Para A., Kay S.A.;
RT "A functional genomics approach reveals CHE as a component of the
RT Arabidopsis circadian clock.";
RL Science 323:1481-1485(2009).
RN [13]
RP INDUCTION.
RX PubMed=20233950; DOI=10.1105/tpc.109.072892;
RA Nakamichi N., Kiba T., Henriques R., Mizuno T., Chua N.H., Sakakibara H.;
RT "PSEUDO-RESPONSE REGULATORS 9, 7, and 5 are transcriptional repressors in
RT the Arabidopsis circadian clock.";
RL Plant Cell 22:594-605(2010).
RN [14]
RP INTERACTION WITH LNK1 AND LNK2.
RX PubMed=25012192; DOI=10.1105/tpc.114.126573;
RA Xie Q., Wang P., Liu X., Yuan L., Wang L., Zhang C., Li Y., Xing H.,
RA Zhi L., Yue Z., Zhao C., McClung C.R., Xu X.;
RT "LNK1 and LNK2 are transcriptional coactivators in the Arabidopsis
RT circadian oscillator.";
RL Plant Cell 26:2843-2857(2014).
RN [15]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. Columbia;
RX PubMed=31429787; DOI=10.1186/s13059-019-1777-1;
RA Song Q., Huang T.-Y., Yu H.H., Ando A., Mas P., Ha M., Chen Z.J.;
RT "Diurnal regulation of SDG2 and JMJ14 by circadian clock oscillators
RT orchestrates histone modification rhythms in Arabidopsis.";
RL Genome Biol. 20:RESEARCH170.1-RESEARCH170.12(2019).
CC -!- FUNCTION: Transcription factor involved in the circadian clock. Binds
CC to the promoter region of APRR1/TOC1 and TCP21/CHE to repress their
CC transcription. Represses both CCA1 and itself. May recognize the
CC promoter of JMJ14 to regulates its expression during the night in a
CC circadian manner (PubMed:31429787). {ECO:0000269|PubMed:12015970,
CC ECO:0000269|PubMed:19095940, ECO:0000269|PubMed:19218364,
CC ECO:0000269|PubMed:31429787, ECO:0000269|PubMed:9657154}.
CC -!- SUBUNIT: Homodimer or heterodimer with CCA1. Interacts with CCA1 (via
CC internal domain); independently of photoperiod. Functions probably as
CC part of a large complex. Interacts with CKB1 and CKB3. Interacts with
CC LNK1 and LNK2 (PubMed:25012192). {ECO:0000269|PubMed:10535927,
CC ECO:0000269|PubMed:19218364, ECO:0000269|PubMed:19339503,
CC ECO:0000269|PubMed:25012192}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00625,
CC ECO:0000269|PubMed:19218364}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=1;
CC Comment=A number of isoforms are produced. According to EST
CC sequences.;
CC Name=1;
CC IsoId=Q6R0H1-1; Sequence=Displayed;
CC -!- TISSUE SPECIFICITY: Expressed in leaves, roots, stems, flowers and
CC siliques. {ECO:0000269|PubMed:19095940, ECO:0000269|PubMed:19218364}.
CC -!- INDUCTION: Circadian-regulation with peak levels occurring around 1
CC hour after dawn. Up-regulated by APRR1/TOC1 and transiently by light
CC treatment. Down-regulated by APRR5, APRR7 and APRR9.
CC {ECO:0000269|PubMed:12574129, ECO:0000269|PubMed:19095940,
CC ECO:0000269|PubMed:19218364, ECO:0000269|PubMed:19286557,
CC ECO:0000269|PubMed:20233950, ECO:0000269|PubMed:9657154}.
CC -!- PTM: Phosphorylated by CK2. {ECO:0000269|PubMed:10535927}.
CC -!- DISRUPTION PHENOTYPE: Shorter circadian oscillations (PubMed:12015970,
CC PubMed:19218364). The double mutant cca1 lhy accumulates higher levels
CC of JMJ14 but lower levels of ATXR3/SDG2, and exhibits damped H3K4me3
CC levels near the transcription start sites of genic regions
CC (PubMed:31429787). {ECO:0000269|PubMed:12015970,
CC ECO:0000269|PubMed:19218364, ECO:0000269|PubMed:31429787}.
CC -!- MISCELLANEOUS: CCA1 and LHY are only partially redundant, but they bind
CC to the same region of the promoters.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAF26474.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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; AJ006404; CAA07004.1; -; mRNA.
DR EMBL; AY519507; AAS09977.1; -; mRNA.
DR EMBL; AC007323; AAF26474.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002684; AEE27223.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE27224.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE27225.1; -; Genomic_DNA.
DR EMBL; CP002684; ANM58172.1; -; Genomic_DNA.
DR EMBL; CP002684; ANM58174.1; -; Genomic_DNA.
DR EMBL; AK316728; BAH19454.1; -; mRNA.
DR EMBL; AK316829; BAH19541.1; -; mRNA.
DR RefSeq; NP_001030924.1; NM_001035847.1. [Q6R0H1-1]
DR RefSeq; NP_001320627.1; NM_001331247.1. [Q6R0H1-1]
DR RefSeq; NP_001320629.1; NM_001331248.1. [Q6R0H1-1]
DR RefSeq; NP_171614.1; NM_099988.4. [Q6R0H1-1]
DR RefSeq; NP_849568.1; NM_179237.1. [Q6R0H1-1]
DR AlphaFoldDB; Q6R0H1; -.
DR SMR; Q6R0H1; -.
DR BioGRID; 24576; 22.
DR IntAct; Q6R0H1; 8.
DR STRING; 3702.AT1G01060.2; -.
DR iPTMnet; Q6R0H1; -.
DR PaxDb; Q6R0H1; -.
DR ProteomicsDB; 238382; -. [Q6R0H1-1]
DR EnsemblPlants; AT1G01060.1; AT1G01060.1; AT1G01060. [Q6R0H1-1]
DR EnsemblPlants; AT1G01060.2; AT1G01060.2; AT1G01060. [Q6R0H1-1]
DR EnsemblPlants; AT1G01060.3; AT1G01060.3; AT1G01060. [Q6R0H1-1]
DR EnsemblPlants; AT1G01060.7; AT1G01060.7; AT1G01060. [Q6R0H1-1]
DR EnsemblPlants; AT1G01060.8; AT1G01060.8; AT1G01060. [Q6R0H1-1]
DR GeneID; 839341; -.
DR Gramene; AT1G01060.1; AT1G01060.1; AT1G01060. [Q6R0H1-1]
DR Gramene; AT1G01060.2; AT1G01060.2; AT1G01060. [Q6R0H1-1]
DR Gramene; AT1G01060.3; AT1G01060.3; AT1G01060. [Q6R0H1-1]
DR Gramene; AT1G01060.7; AT1G01060.7; AT1G01060. [Q6R0H1-1]
DR Gramene; AT1G01060.8; AT1G01060.8; AT1G01060. [Q6R0H1-1]
DR KEGG; ath:AT1G01060; -.
DR Araport; AT1G01060; -.
DR TAIR; locus:2200970; AT1G01060.
DR eggNOG; KOG0724; Eukaryota.
DR InParanoid; Q6R0H1; -.
DR OMA; NVNTQFH; -.
DR PhylomeDB; Q6R0H1; -.
DR PRO; PR:Q6R0H1; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q6R0H1; baseline and differential.
DR Genevisible; Q6R0H1; AT.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0003700; F:DNA-binding transcription factor activity; IDA:UniProtKB.
DR GO; GO:0000976; F:transcription cis-regulatory region binding; IDA:UniProtKB.
DR GO; GO:0007623; P:circadian rhythm; IGI:TAIR.
DR GO; GO:0048574; P:long-day photoperiodism, flowering; IGI:TAIR.
DR GO; GO:0042754; P:negative regulation of circadian rhythm; IMP:TAIR.
DR GO; GO:0043433; P:negative regulation of DNA-binding transcription factor activity; IMP:UniProtKB.
DR GO; GO:0042752; P:regulation of circadian rhythm; IMP:UniProtKB.
DR GO; GO:0006355; P:regulation of transcription, DNA-templated; TAS:TAIR.
DR GO; GO:0009409; P:response to cold; IGI:TAIR.
DR CDD; cd00167; SANT; 1.
DR InterPro; IPR009057; Homeobox-like_sf.
DR InterPro; IPR017930; Myb_dom.
DR InterPro; IPR006447; Myb_dom_plants.
DR InterPro; IPR001005; SANT/Myb.
DR InterPro; IPR017884; SANT_dom.
DR Pfam; PF00249; Myb_DNA-binding; 1.
DR SMART; SM00717; SANT; 1.
DR SUPFAM; SSF46689; SSF46689; 1.
DR TIGRFAMs; TIGR01557; myb_SHAQKYF; 1.
DR PROSITE; PS51294; HTH_MYB; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; Biological rhythms; DNA-binding; Nucleus;
KW Phosphoprotein; Reference proteome; Transcription;
KW Transcription regulation.
FT CHAIN 1..645
FT /note="Protein LHY"
FT /id="PRO_0000388998"
FT DOMAIN 19..73
FT /note="HTH myb-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00625"
FT DNA_BIND 46..69
FT /note="H-T-H motif"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00625"
FT REGION 89..127
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 149..212
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 410..437
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 458..500
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 106..127
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 157..195
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 410..434
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 458..479
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 481..500
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 6
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P92973"
FT CONFLICT 98
FT /note="R -> Q (in Ref. 5; BAH19541)"
FT /evidence="ECO:0000305"
FT CONFLICT 408
FT /note="Q -> R (in Ref. 2; AAS09977)"
FT /evidence="ECO:0000305"
FT CONFLICT 411
FT /note="N -> T (in Ref. 1; CAA07004)"
FT /evidence="ECO:0000305"
FT CONFLICT 537
FT /note="I -> V (in Ref. 5; BAH19541)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 645 AA; 70438 MW; DC327F40AB75AAF5 CRC64;
MDTNTSGEEL LAKARKPYTI TKQRERWTED EHERFLEALR LYGRAWQRIE EHIGTKTAVQ
IRSHAQKFFT KLEKEAEVKG IPVCQALDIE IPPPRPKRKP NTPYPRKPGN NGTSSSQVSS
AKDAKLVSSA SSSQLNQAFL DLEKMPFSEK TSTGKENQDE NCSGVSTVNK YPLPTKQVSG
DIETSKTSTV DNAVQDVPKK NKDKDGNDGT TVHSMQNYPW HFHADIVNGN IAKCPQNHPS
GMVSQDFMFH PMREETHGHA NLQATTASAT TTASHQAFPA CHSQDDYRSF LQISSTFSNL
IMSTLLQNPA AHAAATFAAS VWPYASVGNS GDSSTPMSSS PPSITAIAAA TVAAATAWWA
SHGLLPVCAP APITCVPFST VAVPTPAMTE MDTVENTQPF EKQNTALQDQ NLASKSPASS
SDDSDETGVT KLNADSKTND DKIEEVVVTA AVHDSNTAQK KNLVDRSSCG SNTPSGSDAE
TDALDKMEKD KEDVKETDEN QPDVIELNNR KIKMRDNNSN NNATTDSWKE VSEEGRIAFQ
ALFARERLPQ SFSPPQVAEN VNRKQSDTSM PLAPNFKSQD SCAADQEGVV MIGVGTCKSL
KTRQTGFKPY KRCSMEVKES QVGNINNQSD EKVCKRLRLE GEAST
