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Transcription factor LAF1 (Myb-related protein 18) (AtMYB18) (Protein LONG AFTER FAR-RED LIGHT 1)

 LAF1_ARATH              Reviewed;         283 AA.
Q9M0K4; Q9SUI1; Q9ZTF0;
23-NOV-2004, integrated into UniProtKB/Swiss-Prot.
23-NOV-2004, sequence version 2.
25-APR-2018, entry version 133.
RecName: Full=Transcription factor LAF1 {ECO:0000303|PubMed:11581165};
AltName: Full=Myb-related protein 18 {ECO:0000303|PubMed:9839469};
Short=AtMYB18 {ECO:0000303|PubMed:9839469};
AltName: Full=Protein LONG AFTER FAR-RED LIGHT 1 {ECO:0000303|PubMed:11581165};
Name=LAF1 {ECO:0000303|PubMed:11581165};
Synonyms=MYB18 {ECO:0000303|PubMed:9839469};
OrderedLocusNames=At4g25560 {ECO:0000312|Araport:AT4G25560};
ORFNames=M7J2.70 {ECO:0000312|EMBL:CAA18170.1};
Arabidopsis thaliana (Mouse-ear cress).
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;
Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae;
Arabidopsis.
NCBI_TaxID=3702;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, SUBCELLULAR LOCATION,
TISSUE SPECIFICITY, AND MUTAGENESIS OF LYS-258.
PubMed=11581165; DOI=10.1101/gad.915001;
Ballesteros M.L., Bolle C., Lois L.M., Moore J.M.,
Vielle-Calzada J.-P., Grossniklaus U., Chua N.-H.;
"LAF1, a MYB transcription activator for phytochrome A signaling.";
Genes Dev. 15:2613-2625(2001).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Columbia;
PubMed=10617198; DOI=10.1038/47134;
Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G.,
Pohl T., Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N.,
Harris B., Ansorge W., Brandt P., Grivell L.A., Rieger M.,
Weichselgartner M., de Simone V., Obermaier B., Mache R., Mueller M.,
Kreis M., Delseny M., Puigdomenech P., Watson M., Schmidtheini T.,
Reichert B., Portetelle D., Perez-Alonso M., Boutry M., Bancroft I.,
Vos P., Hoheisel J., Zimmermann W., Wedler H., Ridley P.,
Langham S.-A., McCullagh B., Bilham L., Robben J.,
van der Schueren J., Grymonprez B., Chuang Y.-J., Vandenbussche F.,
Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R., Defoor E.,
Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W.,
Mooijman P., Klein Lankhorst R., Rose M., Hauf J., Koetter P.,
Berneiser S., Hempel S., Feldpausch M., Lamberth S., Van den Daele H.,
De Keyser A., Buysshaert C., Gielen J., Villarroel R., De Clercq R.,
van Montagu M., Rogers J., Cronin A., Quail M.A., Bray-Allen S.,
Clark L., Doggett J., Hall S., Kay M., Lennard N., McLay K., Mayes R.,
Pettett A., Rajandream M.A., Lyne M., Benes V., Rechmann S.,
Borkova D., Bloecker H., Scharfe M., Grimm M., Loehnert T.-H.,
Dose S., de Haan M., Maarse A.C., Schaefer M., Mueller-Auer S.,
Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D., Herzl A.,
Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R.,
Schnabl S., Hiller R., Schmidt W., Lecharny A., Aubourg S.,
Chefdor F., Cooke R., Berger C., Monfort A., Casacuberta E.,
Gibbons T., Weber N., Vandenbol M., Bargues M., Terol J., Torres A.,
Perez-Perez A., Purnelle B., Bent E., Johnson S., Tacon D., Jesse T.,
Heijnen L., Schwarz S., Scholler P., Heber S., Francs P., Bielke C.,
Frishman D., Haase D., Lemcke K., Mewes H.-W., Stocker S.,
Zaccaria P., Bevan M., Wilson R.K., de la Bastide M., Habermann K.,
Parnell L., Dedhia N., Gnoj L., Schutz K., Huang E., Spiegel L.,
Sekhon M., Murray J., Sheet P., Cordes M., Abu-Threideh J.,
Stoneking T., Kalicki J., Graves T., Harmon G., Edwards J.,
Latreille P., Courtney L., Cloud J., Abbott A., Scott K., Johnson D.,
Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D.,
Du H., Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C.,
Antonoiu B., Zidanic M., Strong C., Sun H., Lamar B., Yordan C.,
Ma P., Zhong J., Preston R., Vil D., Shekher M., Matero A., Shah R.,
Swaby I.K., O'Shaughnessy A., Rodriguez M., Hoffman J., Till S.,
Granat S., Shohdy N., Hasegawa A., Hameed A., Lodhi M., Johnson A.,
Chen E., Marra M.A., Martienssen R., McCombie W.R.;
"Sequence and analysis of chromosome 4 of the plant Arabidopsis
thaliana.";
Nature 402:769-777(1999).
[3]
GENOME REANNOTATION.
STRAIN=cv. Columbia;
PubMed=27862469; DOI=10.1111/tpj.13415;
Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
Town C.D.;
"Araport11: a complete reannotation of the Arabidopsis thaliana
reference genome.";
Plant J. 89:789-804(2017).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
STRAIN=cv. Columbia;
PubMed=15208423; DOI=10.1104/pp.104.042176;
Gong W., Shen Y.-P., Ma L.-G., Pan Y., Du Y.-L., Wang D.-H.,
Yang J.-Y., Hu L.-D., Liu X.-F., Dong C.-X., Ma L., Chen Y.-H.,
Yang X.-Y., Gao Y., Zhu D., Tan X., Mu J.-Y., Zhang D.-B., Liu Y.-L.,
Dinesh-Kumar S.P., Li Y., Wang X.-P., Gu H.-Y., Qu L.-J., Bai S.-N.,
Lu Y.-T., Li J.-Y., Zhao J.-D., Zuo J., Huang H., Deng X.-W.,
Zhu Y.-X.;
"Genome-wide ORFeome cloning and analysis of Arabidopsis transcription
factor genes.";
Plant Physiol. 135:773-782(2004).
[5]
NUCLEOTIDE SEQUENCE [MRNA] OF 52-283, INDUCTION, AND NOMENCLATURE.
STRAIN=cv. Columbia;
PubMed=9839469; DOI=10.1046/j.1365-313x.1998.00278.x;
Kranz H.D., Denekamp M., Greco R., Jin H.-L., Leyva A., Meissner R.C.,
Petroni K., Urzainqui A., Bevan M., Martin C., Smeekens S.,
Tonelli C., Paz-Ares J., Weisshaar B.;
"Towards functional characterisation of the members of the R2R3-MYB
gene family from Arabidopsis thaliana.";
Plant J. 16:263-276(1998).
[6]
UBIQUITINATION BY COP1.
PubMed=12827204; DOI=10.1038/nature01696;
Seo H.S., Yang J.-Y., Ishikawa M., Bolle C., Ballesteros M.L.,
Chua N.-H.;
"LAF1 ubiquitination by COP1 controls photomorphogenesis and is
stimulated by SPA1.";
Nature 423:995-999(2003).
[7]
GENE FAMILY.
PubMed=16463103; DOI=10.1007/s11103-005-2910-y;
Chen Y., Yang X., He K., Liu M., Li J., Gao Z., Lin Z., Zhang Y.,
Wang X., Qiu X., Shen Y., Zhang L., Deng X., Luo J., Deng X.-W.,
Chen Z., Gu H., Qu L.-J.;
"The MYB transcription factor superfamily of Arabidopsis: expression
analysis and phylogenetic comparison with the rice MYB family.";
Plant Mol. Biol. 60:107-124(2006).
[8]
FUNCTION, DISRUPTION PHENOTYPE, SUBCELLULAR LOCATION, AND INTERACTION
WITH FHY1 AND FHL.
STRAIN=cv. Columbia;
PubMed=19482971; DOI=10.1105/tpc.109.067215;
Yang S.W., Jang I.-C., Henriques R., Chua N.-H.;
"FAR-RED ELONGATED HYPOCOTYL1 and FHY1-LIKE associate with the
Arabidopsis transcription factors LAF1 and HFR1 to transmit
phytochrome A signals for inhibition of hypocotyl elongation.";
Plant Cell 21:1341-1359(2009).
-!- FUNCTION: Transcription factor that promotes photomorphogenesis in
the light by participating in the transmission of phytochrome A
(phyA) signals to downstream responses (PubMed:11581165,
PubMed:19482971). Probably acts by activating expression of light-
induced genes. In darkness, its degradation prevents the
activation of light-induced genes (PubMed:11581165).
{ECO:0000269|PubMed:11581165, ECO:0000269|PubMed:19482971}.
-!- SUBUNIT: Binds to FHY1 and FHL (PubMed:19482971). Interacts with
COP1. {ECO:0000269|PubMed:19482971}.
-!- INTERACTION:
P43254:COP1; NbExp=3; IntAct=EBI-1543309, EBI-301649;
Q9FE22:HFR1; NbExp=6; IntAct=EBI-1543309, EBI-626001;
-!- SUBCELLULAR LOCATION: Nucleus speckle {ECO:0000255|PROSITE-
ProRule:PRU00625, ECO:0000269|PubMed:11581165,
ECO:0000269|PubMed:19482971}.
-!- TISSUE SPECIFICITY: Expressed at very low level. Expressed in
cauline leaves. {ECO:0000269|PubMed:11581165}.
-!- INDUCTION: By hormones or elicitors treatment. By exposure to
abiotic stress. {ECO:0000269|PubMed:9839469}.
-!- PTM: Ubiquitinated by COP1. Ubiquitination takes place in darkness
and leads to its subsequent degradation, thereby preventing to
activate photomorphogenesis signals. Ubiquitination is stimulated
by SPA1. {ECO:0000269|PubMed:12827204}.
-!- DISRUPTION PHENOTYPE: Partially blind to far-red (FR). Impaired
inhibition of hypocotyl elongation and cotyledons expansion under
continuous FR light conditions. {ECO:0000269|PubMed:19482971}.
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EMBL; AL022197; CAA18170.1; -; Genomic_DNA.
EMBL; AL161563; CAB81366.1; -; Genomic_DNA.
EMBL; CP002687; AEE85077.1; -; Genomic_DNA.
EMBL; AY519609; AAS10079.1; -; mRNA.
EMBL; AF062867; AAC83589.1; -; mRNA.
PIR; D85295; D85295.
PIR; T05791; T05791.
PIR; T51639; T51639.
RefSeq; NP_194286.1; NM_118688.3.
UniGene; At.2136; -.
ProteinModelPortal; Q9M0K4; -.
SMR; Q9M0K4; -.
BioGrid; 13948; 5.
IntAct; Q9M0K4; 2.
STRING; 3702.AT4G25560.1; -.
PaxDb; Q9M0K4; -.
PRIDE; Q9M0K4; -.
EnsemblPlants; AT4G25560.1; AT4G25560.1; AT4G25560.
GeneID; 828661; -.
Gramene; AT4G25560.1; AT4G25560.1; AT4G25560.
KEGG; ath:AT4G25560; -.
Araport; AT4G25560; -.
TAIR; locus:2131844; AT4G25560.
eggNOG; KOG0048; Eukaryota.
eggNOG; COG5147; LUCA.
HOGENOM; HOG000237600; -.
InParanoid; Q9M0K4; -.
KO; K09422; -.
OMA; FWSPDED; -.
OrthoDB; EOG09360LHT; -.
PhylomeDB; Q9M0K4; -.
PRO; PR:Q9M0K4; -.
Proteomes; UP000006548; Chromosome 4.
ExpressionAtlas; Q9M0K4; baseline and differential.
Genevisible; Q9M0K4; AT.
GO; GO:0016607; C:nuclear speck; IEA:UniProtKB-SubCell.
GO; GO:0005634; C:nucleus; IDA:UniProtKB.
GO; GO:0003700; F:DNA binding transcription factor activity; ISS:TAIR.
GO; GO:0000981; F:RNA polymerase II transcription factor activity, sequence-specific DNA binding; IBA:GO_Central.
GO; GO:0043565; F:sequence-specific DNA binding; IBA:GO_Central.
GO; GO:0001135; F:transcription factor activity, RNA polymerase II transcription factor recruiting; IBA:GO_Central.
GO; GO:0044212; F:transcription regulatory region DNA binding; IBA:GO_Central.
GO; GO:0030154; P:cell differentiation; IBA:GO_Central.
GO; GO:0010018; P:far-red light signaling pathway; IMP:TAIR.
GO; GO:0045893; P:positive regulation of transcription, DNA-templated; IDA:TAIR.
GO; GO:0009585; P:red, far-red light phototransduction; IEA:UniProtKB-KW.
GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IBA:GO_Central.
GO; GO:0009639; P:response to red or far red light; IMP:TAIR.
GO; GO:0009751; P:response to salicylic acid; IEP:TAIR.
GO; GO:0006351; P:transcription, DNA-templated; IEA:UniProtKB-KW.
CDD; cd00167; SANT; 2.
InterPro; IPR009057; Homeobox-like_sf.
InterPro; IPR017930; Myb_dom.
InterPro; IPR001005; SANT/Myb.
Pfam; PF00249; Myb_DNA-binding; 2.
SMART; SM00717; SANT; 2.
SUPFAM; SSF46689; SSF46689; 1.
PROSITE; PS51294; HTH_MYB; 2.
1: Evidence at protein level;
Activator; Complete proteome; DNA-binding; Nucleus;
Phytochrome signaling pathway; Reference proteome; Repeat;
Transcription; Transcription regulation; Ubl conjugation.
CHAIN 1 283 Transcription factor LAF1.
/FTId=PRO_0000197074.
DOMAIN 7 59 HTH myb-type 1. {ECO:0000255|PROSITE-
ProRule:PRU00625}.
DOMAIN 60 114 HTH myb-type 2. {ECO:0000255|PROSITE-
ProRule:PRU00625}.
DNA_BIND 35 59 H-T-H motif. {ECO:0000255|PROSITE-
ProRule:PRU00625}.
DNA_BIND 87 110 H-T-H motif. {ECO:0000255|PROSITE-
ProRule:PRU00625}.
COMPBIAS 117 212 Ser-rich. {ECO:0000255|PROSITE-
ProRule:PRU00016}.
MUTAGEN 258 258 K->R: Abolishes the speckles localization
in the nucleus possibly due to the
absence of sumoylation at this residue.
{ECO:0000269|PubMed:11581165}.
CONFLICT 82 82 S -> P (in Ref. 5; AAC83589).
{ECO:0000305}.
CONFLICT 141 141 K -> E (in Ref. 5; AAC83589).
{ECO:0000305}.
CONFLICT 155 155 F -> L (in Ref. 5; AAC83589).
{ECO:0000305}.
CONFLICT 280 280 S -> P (in Ref. 5; AAC83589).
{ECO:0000305}.
SEQUENCE 283 AA; 32433 MW; A04054C846CF2411 CRC64;
MAKTKYGERH RKGLWSPEED EKLRSFILSY GHSCWTTVPI KAGLQRNGKS CRLRWINYLR
PGLKRDMISA EEEETILTFH SSLGNKWSQI AKFLPGRTDN EIKNYWHSHL KKKWLKSQSL
QDAKSISPPS SSSSSLVACG KRNPETLISN HVFSFQRLLE NKSSSPSQES NGNNSHQCSS
APEIPRLFFS EWLSSSYPHT DYSSEFTDSK HSQAPNVEET LSAYEEMGDV DQFHYNEMMI
NNSNWTLNDI VFGSKCKKQE HHIYREASDC NSSAEFFSPS TTT


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