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

Solyc06g051550.2.1

Common Name

56B23-g3, Fer

Organism

Solanum lycopersicum

Taxonomic ID

4081

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum; Lycopersicon

Family

bHLH

Protein Properties

Length: 305aa MW: 34403.8 Da PI: 4.7227

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Solyc06g051550.2.1	genome	ITAG	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	30.8	5.1e-10	128	171	7	55
HHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS HLH 7 erErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 + Er+RR r+++++ Lr+l+P+ +K++Ka+i A+ Y++ Lq Solyc06g051550.2.1 128 ISERKRRGRMKEKLYALRSLVPNI-----TKMDKASIIGDAILYVQGLQ 171 67*******************7.....7***************98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF47459	5.1E-15	120	185	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profile	PS50888	14.869	121	170	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Gene3D	G3DSA:4.10.280.10	6.5E-15	123	186	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	4.31E-11	123	173	No hit	No description
SMART	SM00353	7.5E-13	127	176	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF00010	1.3E-7	128	171	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0034756	Biological Process	regulation of iron ion transport
GO:0071281	Biological Process	cellular response to iron ion
GO:0071369	Biological Process	cellular response to ethylene stimulus
GO:0071732	Biological Process	cellular response to nitric oxide
GO:0046983	Molecular Function	protein dimerization activity

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0005352	anatomy	xylem
PO:0009025	anatomy	vascular leaf

Sequence ? help Back to Top
Protein Sequence Length: 305 aa Download sequence Send to blast
MESGNASMEN NNVNDIGLIN FLDEDNFEQF IELIRGETAD PIVNFCPNYD CEHMTGCFSA 60 ANAQFEPILS SMDFYDTTLP DPISLYNCEI KLDNNDDEDD DESSGTTATT KMTPTSKGTR 120 TDRSRTLISE RKRRGRMKEK LYALRSLVPN ITKMDKASII GDAILYVQGL QTKAKKLKVE 180 IAEFESSSGI FQNAKKMNFT TYYPAIKRIT KMDINQVEEK GFYVRLICNK GRHIAASLFK 240 ALESLNGFNV QTSNLATSTN DYIFTFTLYV RECHEVDINF GNLKLWIASA FLNQGFDFET 300 SPLV*

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Les.3814	0.0	root\| seed

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Expressed in roots and inflorescence, and to a lower extent, in leaves and stems. In roots, confined to the outer cell layers, specifically in the differentiation zone. Also detected in the endodermis and inner tissues of the central cylinder. {ECO:0000269\|PubMed:12679534, ECO:0000269\|PubMed:15539473, ECO:0000269\|PubMed:15556641}.

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor. Essential protein involved in iron uptake responses. Regulates FRO2 at the level of mRNA accumulation and IRT1 at the level of protein accumulation. Confers enhanced iron mobilization responses at low iron supply. {ECO:0000269\|PubMed:15539473, ECO:0000269\|PubMed:15556641, ECO:0000269\|PubMed:16117851}.

Function -- GeneRIF ? help Back to Top
The results indicate that SlbHLH068, as a putative transcription factor, is involved in iron homeostasis in tomato via an interaction with FER. [PMID: 26070639]

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Solyc06g051550.2.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: In roots by iron deficiency. Repressed by cytokinins. Induced by cold, UV, ethylene (ACC), jasmonic acid (JA), flagellin, and salicylic acid (SA) treatments. {ECO:0000269\|PubMed:12679534, ECO:0000269\|PubMed:15531708, ECO:0000269\|PubMed:15539473, ECO:0000269\|PubMed:15556641, ECO:0000269\|PubMed:18397377}.

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

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AF437878	0.0	Lycopersicon esculentum bHLH transcriptional regulator (fer) mRNA, complete cds

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_001234654.2	0.0	bHLH transcriptional regulator
Swissprot	Q0V7X4	9e-81	FIT_ARATH; Transcription factor FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR
TrEMBL	Q5GA67	0.0	Q5GA67_SOLLC; BHLH transcriptional regulator
STRING	Solyc06g051550.2.1	0.0	(Solanum lycopersicum)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Asterids	OGEA3782	23	40
Representative plant	OGRP7271	11	18

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G28160.1	7e-74	FER-like regulator of iron uptake

Link Out ? help Back to Top
Phytozome	Solyc06g051550.2.1
Entrez Gene	543705

Publications ? help Back to Top
Ling HQ,Bauer P,Bereczky Z,Keller B,Ganal M The tomato fer gene encoding a bHLH protein controls iron-uptake responses in roots. Proc. Natl. Acad. Sci. U.S.A., 2002. 99(21): p. 13938-43 [PMID:12370409] Guyot R, et al. Complex organization and evolution of the tomato pericentromeric region at the FER gene locus. Plant Physiol., 2005. 138(3): p. 1205-15 [PMID:16009996] Wang Y,van der Hoeven RS,Nielsen R,Mueller LA,Tanksley SD Characteristics of the tomato nuclear genome as determined by sequencing undermethylated EcoRI digested fragments. Theor. Appl. Genet., 2005. 112(1): p. 72-84 [PMID:16208505] Schmid NB, et al. Feruloyl-CoA 6'-Hydroxylase1-dependent coumarins mediate iron acquisition from alkaline substrates in Arabidopsis. Plant Physiol., 2014. 164(1): p. 160-72 [PMID:24246380] Doustaly F, et al. Uranium perturbs signaling and iron uptake response in Arabidopsis thaliana roots. Metallomics, 2014. 6(4): p. 809-21 [PMID:24549117] Du J, et al. SlbHLH068 interacts with FER to regulate the iron-deficiency response in tomato. Ann. Bot., 2015. 116(1): p. 23-34 [PMID:26070639] Le CT, et al. ZINC FINGER OF ARABIDOPSIS THALIANA12 (ZAT12) Interacts with FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR (FIT) Linking Iron Deficiency and Oxidative Stress Responses. Plant Physiol., 2016. 170(1): p. 540-57 [PMID:26556796] Yang L, et al. Carbon Monoxide Interacts with Auxin and Nitric Oxide to Cope with Iron Deficiency in Arabidopsis. Front Plant Sci, 2016. 7: p. 112 [PMID:27014280] Zhou C, et al. Paenibacillus polymyxa BFKC01 enhances plant iron absorption via improved root systems and activated iron acquisition mechanisms. Plant Physiol. Biochem., 2016. 105: p. 162-173 [PMID:27105423] Mai HJ,Pateyron S,Bauer P Iron homeostasis in Arabidopsis thaliana: transcriptomic analyses reveal novel FIT-regulated genes, iron deficiency marker genes and functional gene networks. BMC Plant Biol., 2016. 16(1): p. 211 [PMID:27716045] Zhou C, et al. Exogenous Melatonin Improves Plant Iron Deficiency Tolerance via Increased Accumulation of Polyamine-Mediated Nitric Oxide. Int J Mol Sci, 2017. [PMID:27792144] 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] Cui Y, et al. Four IVa bHLH Transcription Factors Are Novel Interactors of FIT and Mediate JA Inhibition of Iron Uptake in Arabidopsis. Mol Plant, 2018. 11(9): p. 1166-1183 [PMID:29960107]