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

AT5G39860.1

Common Name

BHLH136, BNQ1, MYH19.1, PRE1

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: 92aa MW: 10514.9 Da PI: 9.3615

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT5G39860.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	21.9	3.1e-07	22	59	18	54
HHHHHHHCTSCC.C...TTS-STCHHHHHHHHHHHHHH CS HLH 18 safeeLrellPk.askapskKlsKaeiLekAveYIksL 54 + ++Lr++lP+ + +s K s + +L+++++YI++L AT5G39860.1 22 DLVSKLRQILPEiGQRRRSDKASASKVLQETCNYIRNL 59 55689*****999*******************98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50888	9.826	4	59	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Gene3D	G3DSA:4.10.280.10	4.7E-7	21	75	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamily	SSF47459	2.36E-7	22	79	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF00010	1.8E-4	22	59	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:0009640	Biological Process	photomorphogenesis
GO:0009740	Biological Process	gibberellic acid mediated signaling pathway
GO:0009741	Biological Process	response to brassinosteroid
GO:0009742	Biological Process	brassinosteroid mediated signaling pathway
GO:0009826	Biological Process	unidimensional cell growth
GO:0040008	Biological Process	regulation of growth
GO:0048510	Biological Process	regulation of timing of transition from vegetative to reproductive phase
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0005515	Molecular Function	protein binding
GO:0046983	Molecular Function	protein dimerization activity

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0000005	anatomy	cultured plant cell
PO:0000013	anatomy	cauline leaf
PO:0000037	anatomy	shoot apex
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:0009066	anatomy	anther
PO:0020030	anatomy	cotyledon
PO:0020038	anatomy	petiole
PO:0025022	anatomy	collective leaf structure
PO:0025281	anatomy	pollen
PO:0001017	developmental stage	M germinated pollen stage
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: 92 aa Download sequence Send to blast
MSNRRSRQSS SAPRISDNQM IDLVSKLRQI LPEIGQRRRS DKASASKVLQ ETCNYIRNLN 60 REVDNLSERL SQLLESVDED SPEAAVIRSL LM

Expression -- Microarray ? help Back to Top
Source	ID	E-value
Genevisible	249383_at	1e-143
Expression Atlas	AT5G39860	-
AtGenExpress	AT5G39860	-
ATTED-II	AT5G39860	-

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Expressed in roots, leaves, stems and flowers. {ECO:0000269\|PubMed:16527868}.

Functional Description ? help Back to Top
Source	Description
TAIR	Encodes PRE1 (PACLOBUTRAZOL RESISTANCE1). PRE1 and IBH1 form a pair of antagonistic HLH/bHLH transcription factors that function downstream of BZR1 to mediate brassinosteroid regulation of cell elongation. BNQ1 is directly and negatively regulated by AP3 and PI in petals.Required for appropriate regulation of flowering time.
UniProt	Atypical and probable non DNA-binding bHLH transcription factor that integrates multiple signaling pathways to regulate cell elongation and plant development. Binds IBH1, forming a pair of antagonistic bHLH transcription factors that function downstream of BZR1 to mediate brassinosteroid regulation of cell elongation. Regulates light responses by binding and inhibiting the activity of the bHLH transcription factor HFR1, a critical regulator of light signaling and shade avoidance. May have a regulatory role in various aspects of gibberellin-dependent growth and development. {ECO:0000269\|PubMed:16527868, ECO:0000269\|PubMed:20009022, ECO:0000269\|PubMed:20305124, ECO:0000269\|PubMed:23161888, ECO:0000269\|PubMed:23221598}.

Function -- GeneRIF ? help Back to Top
PRE genes may have a regulatory role in gibberellin-dependent development in Arabidopsis thaliana [PRE1]. [PMID: 16527868] PRE1-At IBH1 is a conserved pair of antagonistic HLH/bHLH transcription factors that function downstream of BZR1 to mediate brassinosteroid regulation of cell elongation. [PMID: 20009022] PAR1-PRE1 and PAR1-PIF4 heterodimers form a complex HLH/bHLH network regulating cell elongation and plant development in response to light and hormones. [PMID: 22331621] The expression of IBH1 and PRE1 is regulated by brassinosteroid, gibberellins, and developmental phase dependent factors, indicating that two phytohormones and phase-dependent signals are integrated by this triantagonistic bHLH system. [PMID: 23161888] PRE1 gene expression is controlled by ERECTA signaling through chromatin remodeling. [PMID: 28295392]

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT5G39860.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By gibberellin and epibrassinolide. {ECO:0000269\|PubMed:16527868, ECO:0000269\|PubMed:20009022}.

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

Regulation -- ATRM (Manually Curated Upstream Regulators) ? help Back to Top
Source	Upstream Regulator (A: Activate/R: Repress)
ATRM	AT1G75080 (A)

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT5G39860

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AY088246	1e-155	AY088246.1 Arabidopsis thaliana clone 4734 mRNA, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_198802.1	5e-58	basic helix-loop-helix (bHLH) DNA-binding family protein
Swissprot	Q9FLE9	4e-59	PRE1_ARATH; Transcription factor PRE1
TrEMBL	A0A178UFD8	1e-56	A0A178UFD8_ARATH; PRE1
STRING	AT5G39860.1	2e-57	(Arabidopsis thaliana)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM259	28	225
Representative plant	OGRP1877	12	40

Link Out ? help Back to Top
Phytozome	AT5G39860.1
Entrez Gene	833982
iHOP	AT5G39860
wikigenes	AT5G39860

Publications ? help Back to Top
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] Dal Bosco C, et al. Inactivation of the chloroplast ATP synthase gamma subunit results in high non-photochemical fluorescence quenching and altered nuclear gene expression in Arabidopsis thaliana. J. Biol. Chem., 2004. 279(2): p. 1060-9 [PMID:14576160] 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] Hannah MA,Heyer AG,Hincha DK A global survey of gene regulation during cold acclimation in Arabidopsis thaliana. PLoS Genet., 2005. 1(2): p. e26 [PMID:16121258] Lee S, et al. Overexpression of PRE1 and its homologous genes activates Gibberellin-dependent responses in Arabidopsis thaliana. Plant Cell Physiol., 2006. 47(5): p. 591-600 [PMID:16527868] Hyun Y,Lee I KIDARI, encoding a non-DNA Binding bHLH protein, represses light signal transduction in Arabidopsis thaliana. Plant Mol. Biol., 2006. 61(1-2): p. 283-96 [PMID:16786307] Cao D,Cheng H,Wu W,Soo HM,Peng J Gibberellin mobilizes distinct DELLA-dependent transcriptomes to regulate seed germination and floral development in Arabidopsis. Plant Physiol., 2006. 142(2): p. 509-25 [PMID:16920880] Kleine T,Kindgren P,Benedict C,Hendrickson L,Strand A Genome-wide gene expression analysis reveals a critical role for CRYPTOCHROME1 in the response of Arabidopsis to high irradiance. Plant Physiol., 2007. 144(3): p. 1391-406 [PMID:17478635] 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] Zhang LY, et al. Antagonistic HLH/bHLH transcription factors mediate brassinosteroid regulation of cell elongation and plant development in rice and Arabidopsis. Plant Cell, 2009. 21(12): p. 3767-80 [PMID:20009022] Wang H, et al. Regulation of Arabidopsis brassinosteroid signaling by atypical basic helix-loop-helix proteins. Plant Cell, 2009. 21(12): p. 3781-91 [PMID:20023194] Mara CD,Huang T,Irish VF The Arabidopsis floral homeotic proteins APETALA3 and PISTILLATA negatively regulate the BANQUO genes implicated in light signaling. Plant Cell, 2010. 22(3): p. 690-702 [PMID:20305124] Hao Y,Oh E,Choi G,Liang Z,Wang ZY Interactions between HLH and bHLH factors modulate light-regulated plant development. Mol Plant, 2012. 5(3): p. 688-97 [PMID:22331621] Castelain M,Le Hir R,Bellini C The non-DNA-binding bHLH transcription factor PRE3/bHLH135/ATBS1/TMO7 is involved in the regulation of light signaling pathway in Arabidopsis. Physiol Plant, 2012. 145(3): p. 450-60 [PMID:22339648] Meinke DW A survey of dominant mutations in Arabidopsis thaliana. Trends Plant Sci., 2013. 18(2): p. 84-91 [PMID:22995285] Ikeda M,Fujiwara S,Mitsuda N,Ohme-Takagi M A triantagonistic basic helix-loop-helix system regulates cell elongation in Arabidopsis. Plant Cell, 2012. 24(11): p. 4483-97 [PMID:23161888] Bai MY,Fan M,Oh E,Wang ZY A triple helix-loop-helix/basic helix-loop-helix cascade controls cell elongation downstream of multiple hormonal and environmental signaling pathways in Arabidopsis. Plant Cell, 2012. 24(12): p. 4917-29 [PMID:23221598] Ikeda M,Mitsuda N,Ohme-Takagi M ATBS1 INTERACTING FACTORs negatively regulate Arabidopsis cell elongation in the triantagonistic bHLH system. Plant Signal Behav, 2013. 8(3): p. e23448 [PMID:23333962] Ding Y, et al. Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. BMC Plant Biol., 2013. 13: p. 229 [PMID:24377444] 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] Mao WT, et al. The C-Terminal Sequence and PI motif of the Orchid (Oncidium Gower Ramsey) PISTILLATA (PI) Ortholog Determine its Ability to Bind AP3 Orthologs and Enter the Nucleus to Regulate Downstream Genes Controlling Petal and Stamen Formation. Plant Cell Physiol., 2015. 56(11): p. 2079-99 [PMID:26423960] Cai H, et al. ERECTA signaling controls Arabidopsis inflorescence architecture through chromatin-mediated activation of PRE1 expression. New Phytol., 2017. 214(4): p. 1579-1596 [PMID:28295392] Ezer D, et al. The G-Box Transcriptional Regulatory Code in Arabidopsis. Plant Physiol., 2017. 175(2): p. 628-640 [PMID:28864470] 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]