PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

PlantRegMap/PlantTFDB v5.0

Plant Transcription Factor Database

Transcription Factor Information

Basic Information | Signature Domain | Sequence |

Basic Information? help Back to Top

TF ID

AT3G22170.2

Common Name

CPD45, FHY3, MKA23.12

Organism

Arabidopsis thaliana

Taxonomic ID

3702

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis

Family

FAR1

Protein Properties

Length: 839aa MW: 95996.3 Da PI: 7.0309

Description

far-red elongated hypocotyls 3

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT3G22170.2	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	FAR1	81.6	1.3e-25	84	186	1	91
FAR1 1 kfYneYAkevGFsvrkskskkskrngeitkrtfvCskegkreeekkk............tekerrtraetrtgCkaklkvkkekdgkwevtkleleHn 86 +fY+eY++ +GF++ +++s++sk+++e+++++f Cs++g+++e +k+ e+ +r+ +t+Cka+++vk++ dgkw++++++ eHn AT3G22170.2 84 SFYQEYSRAMGFNTAIQNSRRSKTTREFIDAKFACSRYGTKREYDKSfnrprarqskqdPENMAGRRTCAKTDCKASMHVKRRPDGKWVIHSFVREHN 181 5*****************************************99999999877654444444499999************************ PP FAR1 87 Helap 91 Hel p AT3G22170.2 182 HELLP 186 975 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF03101	1.9E-23	84	186	IPR004330	FAR1 DNA binding domain
Pfam	PF10551	4.8E-24	284	376	IPR018289	MULE transposase domain
PROSITE pattern	PS00591	0	343	353	IPR031158	Glycosyl hydrolases family 10, active site
PROSITE profile	PS50966	9.223	564	600	IPR007527	Zinc finger, SWIM-type
SMART	SM00575	6.7E-7	575	602	IPR006564	Zinc finger, PMZ-type

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0009585	Biological Process	red, far-red light phototransduction
GO:0010018	Biological Process	far-red light signaling pathway
GO:0010218	Biological Process	response to far red light
GO:0042753	Biological Process	positive regulation of circadian rhythm
GO:0045893	Biological Process	positive regulation of transcription, DNA-templated
GO:0005634	Cellular Component	nucleus
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0008270	Molecular Function	zinc ion binding

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0000013	anatomy	cauline leaf
PO:0000037	anatomy	shoot apex
PO:0000084	anatomy	plant sperm cell
PO:0000230	anatomy	inflorescence meristem
PO:0000293	anatomy	guard cell
PO:0008019	anatomy	leaf lamina base
PO:0009005	anatomy	root
PO:0009006	anatomy	shoot system
PO:0009009	anatomy	plant embryo
PO:0009010	anatomy	seed
PO:0009025	anatomy	vascular leaf
PO:0009029	anatomy	stamen
PO:0009030	anatomy	carpel
PO:0009031	anatomy	sepal
PO:0009032	anatomy	petal
PO:0009046	anatomy	flower
PO:0009047	anatomy	stem
PO:0009052	anatomy	flower pedicel
PO:0020030	anatomy	cotyledon
PO:0020038	anatomy	petiole
PO:0020100	anatomy	hypocotyl
PO:0020137	anatomy	leaf apex
PO:0025022	anatomy	collective leaf structure
PO:0025195	anatomy	pollen tube cell
PO:0025281	anatomy	pollen
PO:0001054	developmental stage	vascular leaf senescent stage
PO:0001078	developmental stage	plant embryo cotyledonary stage
PO:0001081	developmental stage	mature plant embryo stage
PO:0001185	developmental stage	plant embryo globular stage
PO:0004507	developmental stage	plant embryo bilateral stage
PO:0007064	developmental stage	LP.12 twelve leaves visible stage
PO:0007095	developmental stage	LP.08 eight leaves visible stage
PO:0007098	developmental stage	LP.02 two leaves visible stage
PO:0007103	developmental stage	LP.10 ten leaves visible stage
PO:0007115	developmental stage	LP.04 four leaves visible stage
PO:0007123	developmental stage	LP.06 six leaves visible stage
PO:0007611	developmental stage	petal differentiation and expansion stage
PO:0007616	developmental stage	flowering stage

Sequence ? help Back to Top
Protein Sequence Length: 839 aa Download sequence Send to blast
MDIDLRLHSG DLCKGDDEDR GLDNVLHNEE DMDIGKIEDV SVEVNTDDSV GMGVPTGELV 60 EYTEGMNLEP LNGMEFESHG EAYSFYQEYS RAMGFNTAIQ NSRRSKTTRE FIDAKFACSR 120 YGTKREYDKS FNRPRARQSK QDPENMAGRR TCAKTDCKAS MHVKRRPDGK WVIHSFVREH 180 NHELLPAQAV SEQTRKIYAA MAKQFAEYKT VISLKSDSKS SFEKGRTLSV ETGDFKILLD 240 FLSRMQSLNS NFFYAVDLGD DQRVKNVFWV DAKSRHNYGS FCDVVSLDTT YVRNKYKMPL 300 AIFVGVNQHY QYMVLGCALI SDESAATYSW LMETWLRAIG GQAPKVLITE LDVVMNSIVP 360 EIFPNTRHCL FLWHVLMKVS ENLGQVVKQH DNFMPKFEKC IYKSGKDEDF ARKWYKNLAR 420 FGLKDDQWMI SLYEDRKKWA PTYMTDVLLA GMSTSQRADS INAFFDKYMH KKTSVQEFVK 480 VYDTVLQDRC EEEAKADSEM WNKQPAMKSP SPFEKSVSEV YTPAVFKKFQ IEVLGAIACS 540 PREENRDATC STFRVQDFEN NQDFMVTWNQ TKAEVSCICR LFEYKGYLCR HTLNVLQCCH 600 LSSIPSQYIL KRWTKDAKSR HFSGEPQQLQ TRLLRYNDLC ERALKLNEEA SLSQESYNIA 660 FLAIEGAIGN CAGINTSGRS LPDVVTSPTQ GLISVEEDNH SRSAGKTSKK KNPTKKRKVN 720 PEQDVMPVAA PESLQQMDKL SPRTVGIESY YGTQQSVQGM VQLNLMGPTR DNFYGNQQTM 780 QGLRQLNSIA PSYDSYYGPQ QGIHGQGVDF FRPANFSYDI RDDPNVRTTQ LHEDASRHS

Sequence ? help Back to Top

Protein Sequence Length: 839 aa Download sequence Send to blast

MDIDLRLHSG DLCKGDDEDR GLDNVLHNEE DMDIGKIEDV SVEVNTDDSV GMGVPTGELV  60
EYTEGMNLEP LNGMEFESHG EAYSFYQEYS RAMGFNTAIQ NSRRSKTTRE FIDAKFACSR  120
YGTKREYDKS FNRPRARQSK QDPENMAGRR TCAKTDCKAS MHVKRRPDGK WVIHSFVREH  180
NHELLPAQAV SEQTRKIYAA MAKQFAEYKT VISLKSDSKS SFEKGRTLSV ETGDFKILLD  240
FLSRMQSLNS NFFYAVDLGD DQRVKNVFWV DAKSRHNYGS FCDVVSLDTT YVRNKYKMPL  300
AIFVGVNQHY QYMVLGCALI SDESAATYSW LMETWLRAIG GQAPKVLITE LDVVMNSIVP  360
EIFPNTRHCL FLWHVLMKVS ENLGQVVKQH DNFMPKFEKC IYKSGKDEDF ARKWYKNLAR  420
FGLKDDQWMI SLYEDRKKWA PTYMTDVLLA GMSTSQRADS INAFFDKYMH KKTSVQEFVK  480
VYDTVLQDRC EEEAKADSEM WNKQPAMKSP SPFEKSVSEV YTPAVFKKFQ IEVLGAIACS  540
PREENRDATC STFRVQDFEN NQDFMVTWNQ TKAEVSCICR LFEYKGYLCR HTLNVLQCCH  600
LSSIPSQYIL KRWTKDAKSR HFSGEPQQLQ TRLLRYNDLC ERALKLNEEA SLSQESYNIA  660
FLAIEGAIGN CAGINTSGRS LPDVVTSPTQ GLISVEEDNH SRSAGKTSKK KNPTKKRKVN  720
PEQDVMPVAA PESLQQMDKL SPRTVGIESY YGTQQSVQGM VQLNLMGPTR DNFYGNQQTM  780
QGLRQLNSIA PSYDSYYGPQ QGIHGQGVDF FRPANFSYDI RDDPNVRTTQ LHEDASRHS

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
At.27725	0.0	floral meristem\| flower\| seed\| silique

Expression -- Microarray ? help Back to Top
Source	ID	E-value
Genevisible	256820_at	1e-170
Expression Atlas	AT3G22170	-
AtGenExpress	AT3G22170	-
ATTED-II	AT3G22170	-

Functional Description ? help Back to Top
Source	Description
TAIR	A component of the PHYA signaling network, mediates the FR-HIR response to far-red light in concert with FAR1.
UniProt	Transcription activator that recognizes and binds to the DNA consensus sequence 5'-CACGCGC-3'. Activates the expression of FHY1 and FHL involved in light responses. When associated with PHYA, protects it from being recognized and degraded by the COP1/SPA complex. Positive regulator of chlorophyll biosynthesis via the activation of HEMB1 gene expression. {ECO:0000269\|PubMed:11889039, ECO:0000269\|PubMed:12753585, ECO:0000269\|PubMed:17012604, ECO:0000269\|PubMed:18033885, ECO:0000269\|PubMed:18715961, ECO:0000269\|PubMed:22634759}.

Function -- GeneRIF ? help Back to Top
FHY3 appears to be a novel gating factor, specifically in gating red light signaling to the clock during daytime [PMID: 17012604] study shows FHY3 & FAR1, which encode proteins related to Mutator-like transposases, act together to modulate phyA signaling by activating transcription of FHY1 & FHL [PMID: 18033885] The zinc finger domain is essential for direct DNA binding of FHY3 in mediating light signaling. The central core transposase domain and C-terminal SWIM domain are essential for the transcriptional regulatory activity of FHY3. [PMID: 18715961] phyA associations with FHY3 and FHY1 protect underphosphorylated phyA from being recognized by the COP1/SPA complex. [PMID: 18722184] Data suggest that FHY3 regulates multiple facets of plant development, thus providing insights into its functions beyond light and circadian pathways. [PMID: 21803941] The fhy3 phenotypes of axillary bud outgrowth suppression and of stress-induced leaf growth retardation both required the AUXIN-RESISTANT1 gene, and are independent of phyA. [PMID: 22540368] Transposase-derived proteins FHY3/FAR1 interact with PHYTOCHROME-INTERACTING FACTOR1 to regulate chlorophyll biosynthesis by modulating HEMB1 during deetiolation in Arabidopsis. [PMID: 22634759] COP1 gene expression in response to photomorphogenic UV-B is controlled by a combinatorial regulation of FHY3 and HY5, and this UV-B-specific working mode of FHY3 and HY5 is distinct from that in far-red light and circadian conditions. [PMID: 23150635] FRS4/CPD25 and FHY3/CPD45 function as a heterodimer that cooperatively activates ARC5. [PMID: 23662592] FHY3 and FAR1 are positive regulators of abscissic acid (ABA) signaling and provide insight into the integration of light and ABA signaling. [PMID: 23946351] domestication of FHY3/FAR1 may enable angiosperms to better integrate various endogenous and exogenous signals for coordinated regulation of growth and development, thus enhancing their fitness and adaptation [PMID: 25956482] this study demonstrates an important role of FHY3 and FAR1 in regulating plant immunity, through integrating chlorophyll biosynthesis and the salicylic acid signaling pathway. [PMID: 25989254] FHY3 and FAR1 directly bind the promoter of MIPS1 to activate its expression and thereby promote inositol biosynthesis to prevent [PMID: 26714049] In shoot apical meristem, FHY3 directly represses CLV3, which consequently regulates WUS to maintain the stem cell pool. [PMID: 27469166] the light-signaling proteins FHY3 and FAR1 influence starch synthesis and starch granule formation through transcriptional activation of ISA2. [PMID: 27859295]

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00078	ChIP-seq	26531826	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT3G22170.2

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Down-regulated after exposure to far-red light. Subject to a negative feedback regulation by PHYA signaling. Up-regulated by white light. {ECO:0000269\|PubMed:11889039, ECO:0000269\|PubMed:18033885, ECO:0000269\|PubMed:22634759}.

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	Retrieve

Regulation -- ATRM (Manually Curated Upstream Regulators) ? help Back to Top
Source	Upstream Regulator (A: Activate/R: Repress)
ATRM	AT4G15090 (A)

Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source	Target Gene (A: Activate/R: Repress)
ATRM	AT2G37678(A), AT2G40080(A), AT5G02200(A)

Interaction -- BIND ? help Back to Top
Source	Intact With	Description
BIND	AT4G15090	FAR1 interacts with FHY3.
BIND	AT3G22170	FHY3 interacts with another molecule of FHY3.

Interaction ? help Back to Top
Source	Intact With
BioGRID	AT3G22170, AT4G15090, AT5G11260, AT1G01060

Phenotype -- Disruption Phenotype ? help Back to Top
Source	Description
UniProt	DISRUPTION PHENOTYPE: Reduced protochlorophyllide levels in darkness and less photobleaching in the light. {ECO:0000269\|PubMed:22634759}.

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT3G22170

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AP001306	0.0	AP001306.1 Arabidopsis thaliana genomic DNA, chromosome 3, P1 clone:MKA23.
GenBank	CP002686	0.0	CP002686.1 Arabidopsis thaliana chromosome 3, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_001118673.1	0.0	far-red elongated hypocotyls 3
Refseq	NP_188856.2	0.0	far-red elongated hypocotyls 3
Swissprot	Q9LIE5	0.0	FHY3_ARATH; Protein FAR-RED ELONGATED HYPOCOTYL 3
TrEMBL	A0A178VJL5	0.0	A0A178VJL5_ARATH; FHY3
STRING	AT3G22170.2	0.0	(Arabidopsis thaliana)

Link Out ? help Back to Top
Phytozome	AT3G22170.2
Entrez Gene	821781
iHOP	AT3G22170
wikigenes	AT3G22170

Publications ? help Back to Top
Desnos T,Puente P,Whitelam GC,Harberd NP FHY1: a phytochrome A-specific signal transducer. Genes Dev., 2001. 15(22): p. 2980-90 [PMID:11711433] Wang H,Deng XW Arabidopsis FHY3 defines a key phytochrome A signaling component directly interacting with its homologous partner FAR1. EMBO J., 2002. 21(6): p. 1339-49 [PMID:11889039] Hudson ME,Lisch DR,Quail PH The FHY3 and FAR1 genes encode transposase-related proteins involved in regulation of gene expression by the phytochrome A-signaling pathway. Plant J., 2003. 34(4): p. 453-71 [PMID:12753585] Lin R,Wang H Arabidopsis FHY3/FAR1 gene family and distinct roles of its members in light control of Arabidopsis development. Plant Physiol., 2004. 136(4): p. 4010-22 [PMID:15591448] Zhou Q, et al. FHL is required for full phytochrome A signaling and shares overlapping functions with FHY1. Plant J., 2005. 43(3): p. 356-70 [PMID:16045472] Allen T, et al. Arabidopsis FHY3 specifically gates phytochrome signaling to the circadian clock. Plant Cell, 2006. 18(10): p. 2506-16 [PMID:17012604] Lin R, et al. Transposase-derived transcription factors regulate light signaling in Arabidopsis. Science, 2007. 318(5854): p. 1302-5 [PMID:18033885] Ascencio-Ib Global analysis of Arabidopsis gene expression uncovers a complex array of changes impacting pathogen response and cell cycle during geminivirus infection. Plant Physiol., 2008. 148(1): p. 436-54 [PMID:18650403] Genoud T, et al. FHY1 mediates nuclear import of the light-activated phytochrome A photoreceptor. PLoS Genet., 2008. 4(8): p. e1000143 [PMID:18670649] Lin R, et al. Discrete and essential roles of the multiple domains of Arabidopsis FHY3 in mediating phytochrome A signal transduction. Plant Physiol., 2008. 148(2): p. 981-92 [PMID:18715961] Saijo Y, et al. Arabidopsis COP1/SPA1 complex and FHY1/FHY3 associate with distinct phosphorylated forms of phytochrome A in balancing light signaling. Mol. Cell, 2008. 31(4): p. 607-13 [PMID:18722184] Wang Y, et al. Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis. Plant Physiol., 2008. 148(3): p. 1201-11 [PMID:18775970] Stephenson PG,Terry MJ Light signalling pathways regulating the Mg-chelatase branchpoint of chlorophyll synthesis during de-etiolation in Arabidopsis thaliana. Photochem. Photobiol. Sci., 2008. 7(10): p. 1243-52 [PMID:18846290] Shen Y, et al. Phytochrome A mediates rapid red light-induced phosphorylation of Arabidopsis FAR-RED ELONGATED HYPOCOTYL1 in a low fluence response. Plant Cell, 2009. 21(2): p. 494-506 [PMID:19208901] Reiland S, et al. Large-scale Arabidopsis phosphoproteome profiling reveals novel chloroplast kinase substrates and phosphorylation networks. Plant Physiol., 2009. 150(2): p. 889-903 [PMID:19376835] Li J, et al. Arabidopsis transcription factor ELONGATED HYPOCOTYL5 plays a role in the feedback regulation of phytochrome A signaling. Plant Cell, 2010. 22(11): p. 3634-49 [PMID:21097709] Li G, et al. Coordinated transcriptional regulation underlying the circadian clock in Arabidopsis. Nat. Cell Biol., 2011. 13(5): p. 616-22 [PMID:21499259] Ouyang X, et al. Genome-wide binding site analysis of FAR-RED ELONGATED HYPOCOTYL3 reveals its novel function in Arabidopsis development. Plant Cell, 2011. 23(7): p. 2514-35 [PMID:21803941] Stirnberg P,Zhao S,Williamson L,Ward S,Leyser O FHY3 promotes shoot branching and stress tolerance in Arabidopsis in an AXR1-dependent manner. Plant J., 2012. 71(6): p. 907-20 [PMID:22540368] Tang W, et al. Transposase-derived proteins FHY3/FAR1 interact with PHYTOCHROME-INTERACTING FACTOR1 to regulate chlorophyll biosynthesis by modulating HEMB1 during deetiolation in Arabidopsis. Plant Cell, 2012. 24(5): p. 1984-2000 [PMID:22634759] Huang X, et al. Arabidopsis FHY3 and HY5 positively mediate induction of COP1 transcription in response to photomorphogenic UV-B light. Plant Cell, 2012. 24(11): p. 4590-606 [PMID:23150635] Gao Y, et al. Arabidopsis FRS4/CPD25 and FHY3/CPD45 work cooperatively to promote the expression of the chloroplast division gene ARC5 and chloroplast division. Plant J., 2013. 75(5): p. 795-807 [PMID:23662592] Tilbrook K, et al. The UVR8 UV-B Photoreceptor: Perception, Signaling and Response. Arabidopsis Book, 2013. 11: p. e0164 [PMID:23864838] Tang W, et al. FAR-RED ELONGATED HYPOCOTYL3 and FAR-RED IMPAIRED RESPONSE1 transcription factors integrate light and abscisic acid signaling in Arabidopsis. Plant Physiol., 2013. 163(2): p. 857-66 [PMID:23946351] Jin J, et al. An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors. Mol. Biol. Evol., 2015. 32(7): p. 1767-73 [PMID:25750178] Chang N,Gao Y,Zhao L,Liu X,Gao H Arabidopsis FHY3/CPD45 regulates far-red light signaling and chloroplast division in parallel. Sci Rep, 2015. 5: p. 9612 [PMID:25872642] Wang C, et al. SCAB3 Is Required for Reorganization of Actin Filaments during Light Quality Changes. J Genet Genomics, 2015. 42(4): p. 161-8 [PMID:25953354] Wang H,Wang H Multifaceted roles of FHY3 and FAR1 in light signaling and beyond. Trends Plant Sci., 2015. 20(7): p. 453-61 [PMID:25956482] Wang W, et al. A pair of light signaling factors FHY3 and FAR1 regulates plant immunity by modulating chlorophyll biosynthesis. J Integr Plant Biol, 2016. 58(1): p. 91-103 [PMID:25989254] Ma L, et al. Arabidopsis FHY3 and FAR1 Regulate Light-Induced myo-Inositol Biosynthesis and Oxidative Stress Responses by Transcriptional Activation of MIPS1. Mol Plant, 2016. 9(4): p. 541-57 [PMID:26714049] Siddiqui H,Khan S,Rhodes BM,Devlin PF FHY3 and FAR1 Act Downstream of Light Stable Phytochromes. Front Plant Sci, 2016. 7: p. 175 [PMID:26941752] Li D, et al. FAR-RED ELONGATED HYPOCOTYL3 activates SEPALLATA2 but inhibits CLAVATA3 to regulate meristem determinacy and maintenance in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A., 2016. 113(33): p. 9375-80 [PMID:27469166] Liu L,Li B,Liu X FAR-RED ELONGATED HYPOCOTYL3 promotes floral meristem determinacy in Arabidopsis. Plant Signal Behav, 2016. 11(10): p. e1238545 [PMID:27660915] Ma L,Xue N,Fu X,Zhang H,Li G Arabidopsis thaliana FAR-RED ELONGATED HYPOCOTYLS3 (FHY3) and FAR-RED-IMPAIRED RESPONSE1 (FAR1) modulate starch synthesis in response to light and sugar. New Phytol., 2017. 213(4): p. 1682-1696 [PMID:27859295] Liu Y, et al. Light and Ethylene Coordinately Regulate the Phosphate Starvation Response through Transcriptional Regulation of PHOSPHATE STARVATION RESPONSE1. Plant Cell, 2017. 29(9): p. 2269-2284 [PMID:28842534] Joly-Lopez Z, et al. Abiotic Stress Phenotypes Are Associated with Conserved Genes Derived from Transposable Elements. Front Plant Sci, 2017. 8: p. 2027 [PMID:29250089]