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

AT4G00120.1

Common Name

BHLH40, EDA33, EN120, F6N15.18, GT140, IND, IND1

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: 198aa MW: 22949.3 Da PI: 7.6909

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT4G00120.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	26.6	1.1e-08	126	167	8	54
HHHHHHHHHHHHHHHHHCTSCC.C...TTS-STCHHHHHHHHHHHHHH CS HLH 8 rErrRRdriNsafeeLrellPk.askapskKlsKaeiLekAveYIksL 54 + rrRR+ri +++ L++++P a K++ a++L +A++Y k L AT4G00120.1 126 VARRRRERISEKIRILKRIVPGgA------KMDTASMLDEAIRYTKFL 167 569****************966......************8877 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50888	14.164	118	167	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Gene3D	G3DSA:4.10.280.10	2.9E-12	123	175	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	2.69E-9	124	172	No hit	No description
SuperFamily	SSF47459	3.79E-13	124	177	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	1.1E-11	124	173	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF00010	4.1E-6	127	167	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:0010197	Biological Process	polar nucleus fusion
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 198 aa Download sequence Send to blast
MENGMYKKKG VCDSCVSSKS RSNHSPKRSM MEPQPHHLLM DWNKANDLLT QEHAAFLNDP 60 HHLMLDPPPE TLIHLDEDEE YDEDMDAMKE MQYMIAVMQP VDIDPATVPK PNRRNVRISD 120 DPQTVVARRR RERISEKIRI LKRIVPGGAK MDTASMLDEA IRYTKFLKRQ VRILQPHSQI 180 GAPMANPSYL CYYHNSQP

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
At.34598	0.0	silique

Expression -- Microarray ? help Back to Top
Source	ID	E-value
GEO	30678557	0.0
Expression Atlas	AT4G00120	-
AtGenExpress	AT4G00120	-

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: After fertilization, it is expressed in stripes about four cells wide at the margins of developing wild-type fruit. Also expressed in the inner valve layer, which becomes lignified later in fruit development. Detected in roots. {ECO:0000269\|PubMed:12679534, ECO:0000269\|PubMed:15035986}.

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription regulator required for seed dispersal. Involved in the differentiation of all three cell types required for fruit dehiscence. Acts as the key regulator in a network including SHP and ALC that controls specification of the valve margin. Works with ALC, SHP, and FUL to allow differentiation of the lignified valve layer, the spring-loaded mechanism of fruit that promotes opening. Regulates the expression of the YJ80 marker. {ECO:0000269\|PubMed:15035986}.

Function -- GeneRIF ? help Back to Top
results demonstrate a cellular mechanism for establishing the distinct cell types and a role for IND in regulating the unequal cell divisions in the seven-layer zone [PMID: 16845525] INDEHISCENT directly binds the promoter of PINOID kinase to regulate auxin transport via the PINFORMED auxin efflux transporters. In this way IND generates an auxin minima at the valve margins, which is required for valve margin development. [PMID: 19478783] Study show that IND may directly regulate SPT expression through variant E-box. [PMID: 20176890] SPT and IND at least partially mediate their joint functions in gynoecium and fruit development by controlling auxin distribution. [PMID: 21990939] INDEHISCENT is part of a regulatory network that specifies valve margin /dehiscence zone identity in Arabidopsis thaliana. [PMID: 23126654] ALCATRAZ is a negative regulator of INDEHISCENT, thereby shedding new light on how ALCATRAZ drives separation layer formation. [PMID: 24004048]

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT4G00120.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By FUL, which restrict its expression to the margins.

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	AT2G42830 (A), AT3G58780 (A), AT5G60910 (R)

Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source	Target Gene (A: Activate/R: Repress)
ATRM	AT3G57510(A), AT4G36930(A), ATMG00160(R)

Regulation -- Hormone ? help Back to Top
Source	Hormone
AHD	auxin

Interaction ? help Back to Top
Source	Intact With
BioGRID	AT4G36930
IntAct	Search O81313

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT4G00120

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AL161471	0.0	AL161471.2 Arabidopsis thaliana DNA chromosome 4, contig fragment No. 1.
GenBank	BT029443	0.0	BT029443.1 Arabidopsis thaliana At4g00120 mRNA, complete cds.
GenBank	CP002687	0.0	CP002687.1 Arabidopsis thaliana chromosome 4 sequence.
GenBank	F6N15	0.0	AF069299.1 Arabidopsis thaliana BAC F6N15.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_191923.1	1e-147	basic helix-loop-helix (bHLH) DNA-binding superfamily protein
Swissprot	O81313	1e-148	IND_ARATH; Transcription factor IND
TrEMBL	A0A178UYM9	1e-144	A0A178UYM9_ARATH; IND1
STRING	AT4G00120.1	1e-147	(Arabidopsis thaliana)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM4449	27	54
Representative plant	OGRP761	15	68

Link Out ? help Back to Top
Phytozome	AT4G00120.1
Entrez Gene	827911
iHOP	AT4G00120
wikigenes	AT4G00120

Publications ? help Back to Top
Ferr Negative regulation of the SHATTERPROOF genes by FRUITFULL during Arabidopsis fruit development. Science, 2000. 289(5478): p. 436-8 [PMID:10903201] Riechmann JL, et al. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science, 2000. 290(5499): p. 2105-10 [PMID:11118137] Han Z, et al. A Fas-associated death domain protein-dependent mechanism mediates the apoptotic action of non-steroidal anti-inflammatory drugs in the human leukemic Jurkat cell line. J. Biol. Chem., 2001. 276(42): p. 38748-54 [PMID:11514566] 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] Liljegren SJ, et al. Control of fruit patterning in Arabidopsis by INDEHISCENT. Cell, 2004. 116(6): p. 843-53 [PMID:15035986] Pagnussat GC, et al. Genetic and molecular identification of genes required for female gametophyte development and function in Arabidopsis. Development, 2005. 132(3): p. 603-14 [PMID:15634699] Robles P,Pelaz S Flower and fruit development in Arabidopsis thaliana. Int. J. Dev. Biol., 2005. 49(5-6): p. 633-43 [PMID:16096970] Wu H,Mori A,Jiang X,Wang Y,Yang M The INDEHISCENT protein regulates unequal cell divisions in Arabidopsis fruit. Planta, 2006. 224(4): p. 971-9 [PMID:16845525] Mitsuda N,Ohme-Takagi M NAC transcription factors NST1 and NST3 regulate pod shattering in a partially redundant manner by promoting secondary wall formation after the establishment of tissue identity. Plant J., 2008. 56(5): p. 768-78 [PMID:18657234] Mummenhoff K,Polster A,M Lepidium as a model system for studying the evolution of fruit development in Brassicaceae. J. Exp. Bot., 2009. 60(5): p. 1503-13 [PMID:19052256] Ogawa M,Kay P,Wilson S,Swain SM ARABIDOPSIS DEHISCENCE ZONE POLYGALACTURONASE1 (ADPG1), ADPG2, and QUARTET2 are Polygalacturonases required for cell separation during reproductive development in Arabidopsis. Plant Cell, 2009. 21(1): p. 216-33 [PMID:19168715] Mitsuda N,Ohme-Takagi M Functional analysis of transcription factors in Arabidopsis. Plant Cell Physiol., 2009. 50(7): p. 1232-48 [PMID:19478073] Sorefan K, et al. A regulated auxin minimum is required for seed dispersal in Arabidopsis. Nature, 2009. 459(7246): p. 583-6 [PMID:19478783] Rehrauer H, et al. AGRONOMICS1: a new resource for Arabidopsis transcriptome profiling. Plant Physiol., 2010. 152(2): p. 487-99 [PMID:20032078] Groszmann M,Bylstra Y,Lampugnani ER,Smyth DR Regulation of tissue-specific expression of SPATULA, a bHLH gene involved in carpel development, seedling germination, and lateral organ growth in Arabidopsis. J. Exp. Bot., 2010. 61(5): p. 1495-508 [PMID:20176890] 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] Irish VF The flowering of Arabidopsis flower development. Plant J., 2010. 61(6): p. 1014-28 [PMID:20409275] Arnaud N, et al. Gibberellins control fruit patterning in Arabidopsis thaliana. Genes Dev., 2010. 24(19): p. 2127-32 [PMID:20889713] Moran CN,Halliday KJ Fruit development: new directions for an old pathway. Curr. Biol., 2010. 20(24): p. R1081-3 [PMID:21172630] Arabidopsis Interactome Mapping Consortium Evidence for network evolution in an Arabidopsis interactome map. Science, 2011. 333(6042): p. 601-7 [PMID:21798944] Girin T, et al. INDEHISCENT and SPATULA interact to specify carpel and valve margin tissue and thus promote seed dispersal in Arabidopsis. Plant Cell, 2011. 23(10): p. 3641-53 [PMID:21990939] Avino M,Kramer EM,Donohue K,Hammel AJ,Hall JC Understanding the basis of a novel fruit type in Brassicaceae: conservation and deviation in expression patterns of six genes. Evodevo, 2012. 3(1): p. 20 [PMID:22943452] Kay P,Groszmann M,Ross JJ,Parish RW,Swain SM Modifications of a conserved regulatory network involving INDEHISCENT controls multiple aspects of reproductive tissue development in Arabidopsis. New Phytol., 2013. 197(1): p. 73-87 [PMID:23126654] M Evidence that an evolutionary transition from dehiscent to indehiscent fruits in Lepidium (Brassicaceae) was caused by a change in the control of valve margin identity genes. Plant J., 2013. 73(5): p. 824-35 [PMID:23173897] Gioia T,Logozzo G,Kami J,Spagnoletti Zeuli P,Gepts P Identification and characterization of a homologue to the Arabidopsis INDEHISCENT gene in common Bean. J. Hered., 2013. 104(2): p. 273-86 [PMID:23235700] Lenser T,Thei Conservation of fruit dehiscence pathways between Lepidium campestre and Arabidopsis thaliana sheds light on the regulation of INDEHISCENT. Plant J., 2013. 76(4): p. 545-56 [PMID:24004048] Pabón-Mora N,Wong GK,Ambrose BA Evolution of fruit development genes in flowering plants. Front Plant Sci, 2014. 5: p. 300 [PMID:25018763] We Convergent targeting of a common host protein-network by pathogen effectors from three kingdoms of life. Cell Host Microbe, 2014. 16(3): p. 364-75 [PMID:25211078] Moubayidin L,Ostergaard L Dynamic control of auxin distribution imposes a bilateral-to-radial symmetry switch during gynoecium development. Curr. Biol., 2014. 24(22): p. 2743-8 [PMID:25455035] Jaradat MR,Ruegger M,Bowling A,Butler H,Cutler AJ A comprehensive transcriptome analysis of silique development and dehiscence in Arabidopsis and Brassica integrating genotypic, interspecies and developmental comparisons. GM Crops Food, 2014. 5(4): p. 302-20 [PMID:25523176] 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 Gelderen K,van Rongen M,Liu A,Otten A,Offringa R An INDEHISCENT-Controlled Auxin Response Specifies the Separation Layer in Early Arabidopsis Fruit. Mol Plant, 2016. 9(6): p. 857-69 [PMID:26995296] Balanzà V,Roig-Villanova I,Di Marzo M,Masiero S,Colombo L Seed abscission and fruit dehiscence required for seed dispersal rely on similar genetic networks. Development, 2016. 143(18): p. 3372-81 [PMID:27510967] Pfannebecker KC,Lange M,Rupp O,Becker A Seed Plant-Specific Gene Lineages Involved in Carpel Development. Mol. Biol. Evol., 2017. 34(4): p. 925-942 [PMID:28087776] He H, et al. CELLULASE6 and MANNANASE7 Affect Cell Differentiation and Silique Dehiscence. Plant Physiol., 2018. 176(3): p. 2186-2201 [PMID:29348141] Simonini S,Stephenson P,Østergaard L A molecular framework controlling style morphology in Brassicaceae. Development, 2018. [PMID:29440299] Li XR,Deb J,Kumar SV,Østergaard L Temperature Modulates Tissue-Specification Program to Control Fruit Dehiscence in Brassicaceae. Mol Plant, 2018. 11(4): p. 598-606 [PMID:29449088]