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

AT5G61270.2

Common Name

BHLH72, EN109, MFB13.4, PIF7

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

bHLH

Protein Properties

Length: 278aa MW: 31069.7 Da PI: 9.9405

Description

phytochrome-interacting factor7

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT5G61270.2	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	50.3	4.4e-16	83	128	5	55
HHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS HLH 5 hnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 hne ErrRRdriN+++ +L++llP+a K +K++iL ++e++k+Lq AT5G61270.2 83 HNESERRRRDRINQRMRTLQKLLPTA-----SKADKVSILDDVIEHLKQLQ 128 ***********************9.....7****************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50888	17.06	78	127	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Gene3D	G3DSA:4.10.280.10	3.7E-17	81	137	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamily	SSF47459	2.22E-18	81	148	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	8.22E-9	83	132	No hit	No description
Pfam	PF00010	2.5E-13	83	128	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	1.9E-16	84	133	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0009585	Biological Process	red, far-red light phototransduction
GO:0009704	Biological Process	de-etiolation
GO:0016607	Cellular Component	nuclear speck
GO:0003690	Molecular Function	double-stranded DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0046983	Molecular Function	protein dimerization activity

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0000293	anatomy	guard cell

Sequence ? help Back to Top
Protein Sequence Length: 278 aa Download sequence Send to blast
MDRWFAVQEE SHRVGHSVTA SASGTNMSWA SFESGRSLKT ARTGDRDYFR SGSETQDTEG 60 DEQETRGEAG RSNGRRGRAA AIHNESERRR RDRINQRMRT LQKLLPTASK ADKVSILDDV 120 IEHLKQLQAQ VQFMSLRANL PQQMMIPQLP PPQSVLSIQH QQQQQQQQQQ QQQQQQQFQM 180 SLLATMARMG MGGGGNGYGG LVPPPPPPPM MVPPMGNRDC TNGSSATLSD PYSAFFAQTM 240 NMDLYNKMAA AIYRQQSDQT TKVNIGMPSS SSNHEKRD

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	86	91	ERRRRD

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
At.29114	0.0	leaf

Expression -- Microarray ? help Back to Top
Source	ID	E-value
GEO	186532632	0.0
Expression Atlas	AT5G61270	-
AtGenExpress	AT5G61270	-

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Barely detectable in dark-grown seedlings. Induced after 2 hours of light exposure.
Uniprot	TISSUE SPECIFICITY: Expressed in flowers. {ECO:0000269\|PubMed:12679534}.

Functional Description ? help Back to Top
Source	Description
TAIR	Basic helix-loop-helix (bHLH) phytochrome interacting factor. Interacts specifically with the far-red lightabsorbing Pfr form of phyB through a conserved domain called the active phyB binding motif. Upon light exposure, PIF7 rapidly migrates to intranuclear speckles, where it colocalizes with phyB. Role as negative regulator of phyB-mediated seedling deetiolation.
UniProt	Transcription factor acting negatively in the phytochrome B signaling pathway under prolonged red light. Regulates PHYB abundance at the post-transcriptional level, possibly via the ubiquitin-proteasome pathway. May regulate the expression of a subset of genes by binding to the G-box motif. {ECO:0000269\|PubMed:15486100, ECO:0000269\|PubMed:18252845}.

Function -- GeneRIF ? help Back to Top
Data provide evidence that the mechanism by which PIF7 operate on the phyB signaling pathway under prolonged red light is through maintaining low phyB protein levels, in an additive or synergistic manner. [PMID: 18252845] PIF7 functions as a transcriptional repressor for DREB1C expression and its activity is regulated by PIF7-interacting factors TIMING OF CAB EXPRESSION1 and Phytochrome B. [PMID: 19837816] New auxin synthesized through a PIF7-regulated pathway is required for shade-induced growth, linking directly the perception of a light quality signal to a rapid growth response. [PMID: 22508725] PIF7 regulates the expression of shade-responsive genes.PIF7 recruits MRG1 and MRG2 that binds H3K4me3/H3K36me3 and brings histone-acetylases to induce histone acetylations to promote expression of shade responsive genes. [PMID: 29187567] Shade-induced nuclear localization of PIF7 is regulated by phosphorylation and 14-3-3 proteins in Arabidopsis. [PMID: 29926790]

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00571	DAP	27203113	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT5G61270.2

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By red light. Stable upon light exposure.

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

Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source	Target Gene (A: Activate/R: Repress)
ATRM	AT4G25470(R), AT4G25490(R)

Interaction ? help Back to Top
Source	Intact With
BioGRID	AT1G09530
IntAct	Search Q570R7

Phenotype -- Disruption Phenotype ? help Back to Top
Source	Description
UniProt	DISRUPTION PHENOTYPE: Plants are hypersensitive to red light, exhibiting shorter hypocotyls and larger cotyledons. {ECO:0000269\|PubMed:18252845}.

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT5G61270

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AJ630484	0.0	AJ630484.1 Arabidopsis thaliana mRNA for hypothetical protein, clone At5g61270.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_001032117.1	0.0	phytochrome-interacting factor7
Refseq	NP_001331793.1	0.0	phytochrome-interacting factor7
Refseq	NP_200935.2	0.0	phytochrome-interacting factor7
Swissprot	Q570R7	0.0	PIF7_ARATH; Transcription factor PIF7
TrEMBL	A0A178UKL9	0.0	A0A178UKL9_ARATH; PIF7
TrEMBL	A0A178UMQ5	0.0	A0A178UMQ5_ARATH; PIF7
TrEMBL	C0SVV2	0.0	C0SVV2_ARATH; Uncharacterized protein At5g61270 (Fragment)
STRING	AT5G61270.1	0.0	(Arabidopsis thaliana)

Link Out ? help Back to Top
Phytozome	AT5G61270.2
Entrez Gene	836248
iHOP	AT5G61270
wikigenes	AT5G61270

Publications ? help Back to Top
Riechmann JL, et al. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science, 2000. 290(5499): p. 2105-10 [PMID:11118137] Heim MA, et al. The basic helix-loop-helix transcription factor family in plants: a genome-wide study of protein structure and functional diversity. Mol. Biol. Evol., 2003. 20(5): p. 735-47 [PMID:12679534] Toledo-Ortiz G,Huq E,Quail PH The Arabidopsis basic/helix-loop-helix transcription factor family. Plant Cell, 2003. 15(8): p. 1749-70 [PMID:12897250] Bailey PC, et al. Update on the basic helix-loop-helix transcription factor gene family in Arabidopsis thaliana. Plant Cell, 2003. 15(11): p. 2497-502 [PMID:14600211] Castelli V, et al. Whole genome sequence comparisons and "full-length" cDNA sequences: a combined approach to evaluate and improve Arabidopsis genome annotation. Genome Res., 2004. 14(3): p. 406-13 [PMID:14993207] Gong W, et al. Genome-wide ORFeome cloning and analysis of Arabidopsis transcription factor genes. Plant Physiol., 2004. 135(2): p. 773-82 [PMID:15208423] Khanna R, et al. A novel molecular recognition motif necessary for targeting photoactivated phytochrome signaling to specific basic helix-loop-helix transcription factors. Plant Cell, 2004. 16(11): p. 3033-44 [PMID:15486100] Osuna D, et al. Temporal responses of transcripts, enzyme activities and metabolites after adding sucrose to carbon-deprived Arabidopsis seedlings. Plant J., 2007. 49(3): p. 463-91 [PMID:17217462] Leivar P, et al. The Arabidopsis phytochrome-interacting factor PIF7, together with PIF3 and PIF4, regulates responses to prolonged red light by modulating phyB levels. Plant Cell, 2008. 20(2): p. 337-52 [PMID:18252845] Jaspers P, et al. Unequally redundant RCD1 and SRO1 mediate stress and developmental responses and interact with transcription factors. Plant J., 2009. 60(2): p. 268-79 [PMID:19548978] Kidokoro S, et al. The phytochrome-interacting factor PIF7 negatively regulates DREB1 expression under circadian control in Arabidopsis. Plant Physiol., 2009. 151(4): p. 2046-57 [PMID:19837816] Skinner MK,Rawls A,Wilson-Rawls J,Roalson EH Basic helix-loop-helix transcription factor gene family phylogenetics and nomenclature. Differentiation, 2010. 80(1): p. 1-8 [PMID:20219281] Josse EM, et al. A DELLA in disguise: SPATULA restrains the growth of the developing Arabidopsis seedling. Plant Cell, 2011. 23(4): p. 1337-51 [PMID:21478445] Bu Q,Castillon A,Chen F,Zhu L,Huq E Dimerization and blue light regulation of PIF1 interacting bHLH proteins in Arabidopsis. Plant Mol. Biol., 2011. 77(4-5): p. 501-11 [PMID:21928113] Li L, et al. Linking photoreceptor excitation to changes in plant architecture. Genes Dev., 2012. 26(8): p. 785-90 [PMID:22508725] Lee CM,Thomashow MF Photoperiodic regulation of the C-repeat binding factor (CBF) cold acclimation pathway and freezing tolerance in Arabidopsis thaliana. Proc. Natl. Acad. Sci. U.S.A., 2012. 109(37): p. 15054-9 [PMID:22927419] Ding Y, et al. Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. BMC Plant Biol., 2013. 13: p. 229 [PMID:24377444] Liu Y,Liu Q,Yan Q,Shi L,Fang Y Nucleolus-tethering system (NoTS) reveals that assembly of photobodies follows a self-organization model. Mol. Biol. Cell, 2014. 25(8): p. 1366-73 [PMID:24554768] Dong J, et al. Arabidopsis DE-ETIOLATED1 represses photomorphogenesis by positively regulating phytochrome-interacting factors in the dark. Plant Cell, 2014. 26(9): p. 3630-45 [PMID:25248553] 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] Qiu Y, et al. HEMERA Couples the Proteolysis and Transcriptional Activity of PHYTOCHROME INTERACTING FACTORs in Arabidopsis Photomorphogenesis. Plant Cell, 2015. 27(5): p. 1409-27 [PMID:25944101] de Wit M,Ljung K,Fankhauser C Contrasting growth responses in lamina and petiole during neighbor detection depend on differential auxin responsiveness rather than different auxin levels. New Phytol., 2015. 208(1): p. 198-209 [PMID:25963518] Bou-Torrent J, et al. Regulation of Carotenoid Biosynthesis by Shade Relies on Specific Subsets of Antagonistic Transcription Factors and Cofactors. Plant Physiol., 2015. 169(3): p. 1584-94 [PMID:26082398] Mizuno T,Oka H,Yoshimura F,Ishida K,Yamashino T Insight into the mechanism of end-of-day far-red light (EODFR)-induced shade avoidance responses in Arabidopsis thaliana. Biosci. Biotechnol. Biochem., 2015. 79(12): p. 1987-94 [PMID:26193333] Huang H, et al. Identification of Evening Complex Associated Proteins in Arabidopsis by Affinity Purification and Mass Spectrometry. Mol. Cell Proteomics, 2016. 15(1): p. 201-17 [PMID:26545401] Paik I,Kathare PK,Kim JI,Huq E Expanding Roles of PIFs in Signal Integration from Multiple Processes. Mol Plant, 2017. 10(8): p. 1035-1046 [PMID:28711729] Peng M, et al. Linking PHYTOCHROME-INTERACTING FACTOR to Histone Modification in Plant Shade Avoidance. Plant Physiol., 2018. 176(2): p. 1341-1351 [PMID:29187567] Huang X, et al. Shade-induced nuclear localization of PIF7 is regulated by phosphorylation and 14-3-3 proteins in Arabidopsis. Elife, 2019. [PMID:29926790]