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

AT3G56980.1

Common Name

BHLH039, bHLH39, EN9, F24I3.60, ORG3

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: 258aa MW: 29003.8 Da PI: 6.9125

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT3G56980.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	49.9	5.8e-16	77	129	1	55
CHHHHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS HLH 1 rrrahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 ++ +hn+ Er RR++iNs f+ Lr++lP + ++skKls +++ + +YI +Lq AT3G56980.1 77 KKLNHNASERDRRRKINSLFSSLRSCLPAS--GQSKKLSIPATVSRSLKYIPELQ 129 6789***********************8..7*****************998 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50888	14.449	76	128	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamily	SSF47459	1.57E-16	77	146	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	8.10E-15	77	132	No hit	No description
Gene3D	G3DSA:4.10.280.10	2.3E-14	77	143	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF00010	2.3E-13	77	129	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	2.9E-12	82	134	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006357	Biological Process	regulation of transcription from RNA polymerase II promoter
GO:0010106	Biological Process	cellular response to iron ion starvation
GO:0055072	Biological Process	iron ion homeostasis
GO:0090575	Cellular Component	RNA polymerase II transcription factor complex
GO:0000977	Molecular Function	RNA polymerase II regulatory region sequence-specific 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:0008019	anatomy	leaf lamina base
PO:0009005	anatomy	root
PO:0009006	anatomy	shoot system
PO:0009015	anatomy	portion of vascular tissue
PO:0009025	anatomy	vascular leaf
PO:0020038	anatomy	petiole
PO:0025022	anatomy	collective leaf structure
PO:0007064	developmental stage	LP.12 twelve leaves visible stage
PO:0007095	developmental stage	LP.08 eight 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

Sequence ? help Back to Top
Protein Sequence Length: 258 aa Download sequence Send to blast
MCALVPPLFP NFGWPSTGEY DSYYLAGDIL NNGGFLDFPV PEETYGAVTA VTQHQNSFGV 60 SVSSEGNEID NNPVVVKKLN HNASERDRRR KINSLFSSLR SCLPASGQSK KLSIPATVSR 120 SLKYIPELQE QVKKLIKKKE ELLVQISGQR NTECYVKQPP KAVANYISTV SATRLGDNEV 180 MVQISSSKIH NFSISNVLSG LEEDRFVLVD MSSSRSQGER LFYTLHLQVE KIENYKLNCE 240 ELSQRMLYLY EECGNSYI

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
At.64158	0.0	flower

Expression -- Microarray ? help Back to Top
Source	ID	E-value
Genevisible	251677_at	0.0
Expression Atlas	AT3G56980	-
AtGenExpress	AT3G56980	-
ATTED-II	AT3G56980	-

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Expressed in vascular tissues. Detected in roots. {ECO:0000269\|PubMed:12679534, ECO:0000269\|PubMed:18296723}.

Functional Description ? help Back to Top
Source	Description
TAIR	Encodes a member of the basic helix-loop-helix transcription factor protein.

Function -- GeneRIF ? help Back to Top
AtbHLH38 and AtbHLH39 are induced under iron deficiency. They are involved in the iron deficiency induced synthesis and excretion of riboflavin or vitamin B2. [AtbHLH39] [PMID: 17260143] up-regulated by iron deficiency in roots and leaves [PMID: 17516080] Data indicate that steady-state mRNA abundance for three representative Fe homeostasis genes, IRT1, bHLH39, and FER1, oscillated in light/dark (LD) cycles or warm/cold environmental cycles. [PMID: 23250624] The authors provide evidence that subgroup transcription factor bHLH039 transcription factor is involved in FIT transcriptional regulation. [PMID: 28883478] Study identified ORG3 as a direct downstream, and positively regulated target of GRF9. Genetic analysis of grf9 org3 and GRF9ox org3 double mutants reveals that both transcription factors act in a regulatory cascade to control the final leaf dimensions by restricting cell number in the developing leaf in Arabidopsis thaliana. [PMID: 29985961]

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT3G56980.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Induced by OBP3, auxin and salicylic acid (SA). Repressed by jasmonic acid (JA). Up regulated by iron deficiency in roots and leaves, as well as by nickel, high zinc or high copper treatments. Repressed by high iron, low copper and low zinc treatments. {ECO:0000269\|PubMed:12887587, ECO:0000269\|PubMed:17516080}.

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	AT1G07640 (A), AT3G55370 (A)

Interaction ? help Back to Top
Source	Intact With
BioGRID	AT5G11260
IntAct	Search Q9M1K0

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT3G56980

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AF488577	0.0	AF488577.1 Arabidopsis thaliana clone bHLH039 putative bHLH transcription factor mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_191257.1	0.0	basic helix-loop-helix (bHLH) DNA-binding superfamily protein
Swissprot	Q9M1K0	0.0	ORG3_ARATH; Transcription factor ORG3
TrEMBL	A0A178VCL5	0.0	A0A178VCL5_ARATH; ORG3
STRING	AT3G56980.1	0.0	(Arabidopsis thaliana)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM482	28	153
Representative plant	OGRP2826	11	29

Link Out ? help Back to Top
Phytozome	AT3G56980.1
Entrez Gene	824865
iHOP	AT3G56980
wikigenes	AT3G56980

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] Kang HG,Foley RC,Oñate-Sánchez L,Lin C,Singh KB Target genes for OBP3, a Dof transcription factor, include novel basic helix-loop-helix domain proteins inducible by salicylic acid. Plant J., 2003. 35(3): p. 362-72 [PMID:12887587] 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] Czechowski T,Bari RP,Stitt M,Scheible WR,Udvardi MK Real-time RT-PCR profiling of over 1400 Arabidopsis transcription factors: unprecedented sensitivity reveals novel root- and shoot-specific genes. Plant J., 2004. 38(2): p. 366-79 [PMID:15078338] M Changes in gene expression in response to altered SHL transcript levels. Plant Mol. Biol., 2003. 53(6): p. 805-20 [PMID:15082927] S ABA activates ADPR cyclase and cADPR induces a subset of ABA-responsive genes in Arabidopsis. Plant J., 2004. 38(3): p. 381-95 [PMID:15086800] Zhao C,Craig JC,Petzold HE,Dickerman AW,Beers EP The xylem and phloem transcriptomes from secondary tissues of the Arabidopsis root-hypocotyl. Plant Physiol., 2005. 138(2): p. 803-18 [PMID:15923329] Fujita Y, et al. AREB1 Is a transcription activator of novel ABRE-dependent ABA signaling that enhances drought stress tolerance in Arabidopsis. Plant Cell, 2005. 17(12): p. 3470-88 [PMID:16284313] Yoine M,Ohto MA,Onai K,Mita S,Nakamura K The lba1 mutation of UPF1 RNA helicase involved in nonsense-mediated mRNA decay causes pleiotropic phenotypic changes and altered sugar signalling in Arabidopsis. Plant J., 2006. 47(1): p. 49-62 [PMID:16740149] 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] Tran LS, et al. Co-expression of the stress-inducible zinc finger homeodomain ZFHD1 and NAC transcription factors enhances expression of the ERD1 gene in Arabidopsis. Plant J., 2007. 49(1): p. 46-63 [PMID:17233795] Vorwieger A, et al. Iron assimilation and transcription factor controlled synthesis of riboflavin in plants. Planta, 2007. 226(1): p. 147-58 [PMID:17260143] Sottosanto JB,Saranga Y,Blumwald E Impact of AtNHX1, a vacuolar Na+/H+ antiporter, upon gene expression during short- and long-term salt stress in Arabidopsis thaliana. BMC Plant Biol., 2007. 7: p. 18 [PMID:17411438] Wang HY, et al. Iron deficiency-mediated stress regulation of four subgroup Ib BHLH genes in Arabidopsis thaliana. Planta, 2007. 226(4): p. 897-908 [PMID:17516080] Yuan Y, et al. FIT interacts with AtbHLH38 and AtbHLH39 in regulating iron uptake gene expression for iron homeostasis in Arabidopsis. Cell Res., 2008. 18(3): p. 385-97 [PMID:18268542] Wenzel CL,Hester Q,Mattsson J Identification of genes expressed in vascular tissues using NPA-induced vascular overgrowth in Arabidopsis. Plant Cell Physiol., 2008. 49(3): p. 457-68 [PMID:18296723] Krishnaswamy SS, et al. Transcriptional profiling of pea ABR17 mediated changes in gene expression in Arabidopsis thaliana. BMC Plant Biol., 2008. 8: p. 91 [PMID:18783601] Gong W, et al. The development of protein microarrays and their applications in DNA-protein and protein-protein interaction analyses of Arabidopsis transcription factors. Mol Plant, 2008. 1(1): p. 27-41 [PMID:19802365] 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] Ivanov R,Brumbarova T,Bauer P Fitting into the harsh reality: regulation of iron-deficiency responses in dicotyledonous plants. Mol Plant, 2012. 5(1): p. 27-42 [PMID:21873619] Wang N, et al. Requirement and functional redundancy of Ib subgroup bHLH proteins for iron deficiency responses and uptake in Arabidopsis thaliana. Mol Plant, 2013. 6(2): p. 503-13 [PMID:22983953] Sivitz AB,Hermand V,Curie C,Vert G Arabidopsis bHLH100 and bHLH101 control iron homeostasis via a FIT-independent pathway. PLoS ONE, 2012. 7(9): p. e44843 [PMID:22984573] Hong S,Kim SA,Guerinot ML,McClung CR Reciprocal interaction of the circadian clock with the iron homeostasis network in Arabidopsis. Plant Physiol., 2013. 161(2): p. 893-903 [PMID:23250624] Matsuoka K, et al. Gibberellin-induced expression of Fe uptake-related genes in Arabidopsis. Plant Cell Physiol., 2014. 55(1): p. 87-98 [PMID:24192296] Maurer F,Naranjo Arcos MA,Bauer P Responses of a triple mutant defective in three iron deficiency-induced Basic Helix-Loop-Helix genes of the subgroup Ib(2) to iron deficiency and salicylic acid. PLoS ONE, 2014. 9(6): p. e99234 [PMID:24919188] Martínez-Trujillo M, et al. Chromate alters root system architecture and activates expression of genes involved in iron homeostasis and signaling in Arabidopsis thaliana. Plant Mol. Biol., 2014. 86(1-2): p. 35-50 [PMID:24928490] 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] Van Dingenen J, et al. Strobilurins as growth-promoting compounds: how Stroby regulates Arabidopsis leaf growth. Plant Cell Environ., 2017. 40(9): p. 1748-1760 [PMID:28444690] Ezer D, et al. The G-Box Transcriptional Regulatory Code in Arabidopsis. Plant Physiol., 2017. 175(2): p. 628-640 [PMID:28864470] Naranjo-Arcos MA, et al. Dissection of iron signaling and iron accumulation by overexpression of subgroup Ib bHLH039 protein. Sci Rep, 2017. 7(1): p. 10911 [PMID:28883478] Kailasam S,Wang Y,Lo JC,Chang HF,Yeh KC S-Nitrosoglutathione works downstream of nitric oxide to mediate iron-deficiency signaling in Arabidopsis. Plant J., 2018. 94(1): p. 157-168 [PMID:29396986] Kurt F,Filiz E Genome-wide and comparative analysis of bHLH38, bHLH39, bHLH100 and bHLH101 genes in Arabidopsis, tomato, rice, soybean and maize: insights into iron (Fe) homeostasis. Biometals, 2018. 31(4): p. 489-504 [PMID:29546482] Omidbakhshfard MA, et al. GROWTH-REGULATING FACTOR 9 negatively regulates arabidopsis leaf growth by controlling ORG3 and restricting cell proliferation in leaf primordia. PLoS Genet., 2018. 14(7): p. e1007484 [PMID:29985961]