PlantTFDB
Plant Transcription Factor Database
v4.0
Previous version: v1.0, v2.0, v3.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT2G28160.1
Common NameATBHLH029, ATBHLH29, ATFIT1, BHLH029, BHLH29, EN43, F24D13.5, FIT, FIT1, FRU
Organism
Taxonomic ID
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: 318aa    MW: 35520.5 Da    PI: 4.3576
Description FER-like regulator of iron uptake
Gene Model
Gene Model ID Type Source Coding Sequence
AT2G28160.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1HLH34.53.7e-11134177755
                  HHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS
          HLH   7 erErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 
                  + ErrRR r+++++  Lr+l+P+      +K++Ka+i+  Av Y+++Lq
  AT2G28160.1 134 ISERRRRGRMKDKLYALRSLVPNI-----TKMDKASIVGDAVLYVQELQ 177
                  67*********************7.....7******************9 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF474595.89E-16127194IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profilePS5088815.193127176IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene3DG3DSA:4.10.280.105.5E-16129196IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
CDDcd000832.08E-12129179No hitNo description
SMARTSM003533.1E-14133182IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PfamPF000101.2E-8134177IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0034756Biological Processregulation of iron ion transport
GO:0071281Biological Processcellular response to iron ion
GO:0071369Biological Processcellular response to ethylene stimulus
GO:0071732Biological Processcellular response to nitric oxide
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0005515Molecular Functionprotein binding
GO:0046983Molecular Functionprotein dimerization activity
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000293anatomyguard cell
PO:0009005anatomyroot
Sequence ? help Back to Top
Protein Sequence    Length: 318 aa     Download sequence    Send to blast
MEGRVNALSN INDLELHNFL VDPNFDQFIN LIRGDHQTID ENPVLDFDLG PLQNSPCFID  60
ENQFIPTPVD DLFDELPDLD SNVAESFRSF DGDSVRAGGE EDEEDYNDGD DSSATTTNND  120
GTRKTKTDRS RTLISERRRR GRMKDKLYAL RSLVPNITKM DKASIVGDAV LYVQELQSQA  180
KKLKSDIAGL EASLNSTGGY QEHAPDAQKT QPFRGINPPA SKKIIQMDVI QVEEKGFYVR  240
LVCNKGEGVA PSLYKSLESL TSFQVQNSNL SSPSPDTYLL TYTLDGTCFE QSLNLPNLKL  300
WITGSLLNQG FEFIKSFT
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.435100.0leaf| root
Expression -- Microarray ? help Back to Top
Source ID E-value
Genevisible266162_at0.0
Expression AtlasAT2G28160-
AtGenExpressAT2G28160-
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE 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
TAIREncodes a putative transcription factor that regulates iron uptake responses. mRNA is detected in the outer cell layers of the root and accumulates in response to iron deficiency. The expression of many iron-regulated genes is dependent on FIT1. It specifically regulates FRO2 at the level of mRNA accumulation and IRT1 at the level of protein accumulation.Similar to FER in tomato and is a regulator of iron uptake.
UniProtTranscription 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
  1. We propose a new model for iron uptake in Arabidopsis where FRO2 and IRT1 are differentially regulated by FIT1 which encodes a putative transcription factor that regulates iron uptake responses in Arabidopsis thaliana
    [PMID: 15539473]
  2. AtbHLH29 encods a bHLH protein, which is a functional ortholog of the tomato FER gene which are proposed as transcriptional factors functioning in iron deficiency responses and iron uptake.
    [PMID: 16117851]
  3. A proposed common name for At2g28160 in Arabidopsis, namely FIT=FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR, is discussed.
    [PMID: 17466530]
  4. ferric-chelate reductase FRO2 and ferrous-transporter IRT1 are the targets of the three transcription factors and the transcription of FRO2 and IRT1 is directly regulated by a complex of FIT/AtbHLH38 or FIT/AtbHLH39.
    [PMID: 18268542]
  5. FIT is post-translationally regulated by iron deficiency, leading to a decrease in FIT protein stability mediated by proteasome-dependent degradation.
    [PMID: 21426424]
  6. EIN3/EIL1 physically interact with FIT, are required for full FIT accumulation, and contribute to full FIT downstream target gene expression.
    [PMID: 21586684]
  7. Nitric oxide as a signal that promoted not only the activation of FIT but also its protein stability, independent of the transcriptional control by ethylene and Nitric oxide.
    [PMID: 21972265]
  8. bHLH100 and bHLH101 are key regulators of iron-deficiency responses independent of the master regulator FIT
    [PMID: 22984573]
  9. FER-like iron deficiency-induced transcription factor functions as a direct or indirect modulator of protein levels of a subset of gene products under iron deficiency.
    [PMID: 25951126]
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT2G28160.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: 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
PlantRegMapRetrieveRetrieve
Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source Target Gene (A: Activate/R: Repress)
ATRM AT1G01580(A), AT3G58810(R), AT3G60330(A), AT5G03570(A)
Interaction ? help Back to Top
Source Intact With
BioGRIDAT2G41240, AT3G20770, AT5G04150
IntActSearch Q0V7X4
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT2G28160
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankBT0264460.0BT026446.1 Arabidopsis thaliana At2g28160 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_850114.10.0FER-LIKE IRON DEFICIENCY-INDUCED transcription factor
SwissprotQ0V7X40.0FIT_ARATH; Transcription factor FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR
TrEMBLC0SV650.0C0SV65_ARATH; Putative uncharacterized protein At2g28160 (Fragment)
STRINGAT2G28160.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Representative plantOGRP72711118
MalvidsOGEM41872857
Publications ? help Back to Top
  1. Riechmann JL, et al.
    Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
    Science, 2000. 290(5499): p. 2105-10
    [PMID:11118137]
  2. 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]
  3. 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]
  4. Rashotte AM,Carson SD,To JP,Kieber JJ
    Expression profiling of cytokinin action in Arabidopsis.
    Plant Physiol., 2003. 132(4): p. 1998-2011
    [PMID:12913156]
  5. 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]
  6. Bauer P, et al.
    Analysis of sequence, map position, and gene expression reveals conserved essential genes for iron uptake in Arabidopsis and tomato.
    Plant Physiol., 2004. 136(4): p. 4169-83
    [PMID:15531708]
  7. Colangelo EP,Guerinot ML
    The essential basic helix-loop-helix protein FIT1 is required for the iron deficiency response.
    Plant Cell, 2004. 16(12): p. 3400-12
    [PMID:15539473]
  8. Jakoby M,Wang HY,Reidt W,Weisshaar B,Bauer P
    FRU (BHLH029) is required for induction of iron mobilization genes in Arabidopsis thaliana.
    FEBS Lett., 2004. 577(3): p. 528-34
    [PMID:15556641]
  9. Yuan YX,Zhang J,Wang DW,Ling HQ
    AtbHLH29 of Arabidopsis thaliana is a functional ortholog of tomato FER involved in controlling iron acquisition in strategy I plants.
    Cell Res., 2005. 15(8): p. 613-21
    [PMID:16117851]
  10. Taki N, et al.
    12-oxo-phytodienoic acid triggers expression of a distinct set of genes and plays a role in wound-induced gene expression in Arabidopsis.
    Plant Physiol., 2005. 139(3): p. 1268-83
    [PMID:16258017]
  11. Arrivault S,Senger T,Kr
    The Arabidopsis metal tolerance protein AtMTP3 maintains metal homeostasis by mediating Zn exclusion from the shoot under Fe deficiency and Zn oversupply.
    Plant J., 2006. 46(5): p. 861-79
    [PMID:16709200]
  12. Schaaf G, et al.
    AtIREG2 encodes a tonoplast transport protein involved in iron-dependent nickel detoxification in Arabidopsis thaliana roots.
    J. Biol. Chem., 2006. 281(35): p. 25532-40
    [PMID:16790430]
  13. Lee DJ, et al.
    Genome-wide expression profiling of ARABIDOPSIS RESPONSE REGULATOR 7(ARR7) overexpression in cytokinin response.
    Mol. Genet. Genomics, 2007. 277(2): p. 115-37
    [PMID:17061125]
  14. Bauer P,Ling HQ,Guerinot ML
    FIT, the FER-LIKE IRON DEFICIENCY INDUCED TRANSCRIPTION FACTOR in Arabidopsis.
    Plant Physiol. Biochem., 2007. 45(5): p. 260-1
    [PMID:17466530]
  15. 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]
  16. 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]
  17. S
    Cytokinins negatively regulate the root iron uptake machinery in Arabidopsis through a growth-dependent pathway.
    Plant J., 2008. 55(2): p. 289-300
    [PMID:18397377]
  18. Shen J,Xu X,Li T,Cao D,Han Z
    An MYB transcription factor from Malus xiaojinensis has a potential role in iron nutrition.
    J Integr Plant Biol, 2008. 50(10): p. 1300-6
    [PMID:19017117]
  19. Zhang H, et al.
    A soil bacterium regulates plant acquisition of iron via deficiency-inducible mechanisms.
    Plant J., 2009. 58(4): p. 568-77
    [PMID:19154225]
  20. Kong WW,Zhang LP,Guo K,Liu ZP,Yang ZM
    Carbon monoxide improves adaptation of Arabidopsis to iron deficiency.
    Plant Biotechnol. J., 2010. 8(1): p. 88-99
    [PMID:20055961]
  21. Garc
    Ethylene and nitric oxide involvement in the up-regulation of key genes related to iron acquisition and homeostasis in Arabidopsis.
    J. Exp. Bot., 2010. 61(14): p. 3885-99
    [PMID:20627899]
  22. Maurer F,M
    Suppression of Fe deficiency gene expression by jasmonate.
    Plant Physiol. Biochem., 2011. 49(5): p. 530-6
    [PMID:21334215]
  23. Sivitz A,Grinvalds C,Barberon M,Curie C,Vert G
    Proteasome-mediated turnover of the transcriptional activator FIT is required for plant iron-deficiency responses.
    Plant J., 2011. 66(6): p. 1044-52
    [PMID:21426424]
  24. Lingam S, et al.
    Interaction between the bHLH transcription factor FIT and ETHYLENE INSENSITIVE3/ETHYLENE INSENSITIVE3-LIKE1 reveals molecular linkage between the regulation of iron acquisition and ethylene signaling in Arabidopsis.
    Plant Cell, 2011. 23(5): p. 1815-29
    [PMID:21586684]
  25. 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]
  26. Meiser J,Lingam S,Bauer P
    Posttranslational regulation of the iron deficiency basic helix-loop-helix transcription factor FIT is affected by iron and nitric oxide.
    Plant Physiol., 2011. 157(4): p. 2154-66
    [PMID:21972265]
  27. Meiser J,Bauer P
    Looking for the hub in Fe signaling.
    Plant Signal Behav, 2012. 7(6): p. 688-90
    [PMID:22580691]
  28. 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]
  29. 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]
  30. 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]
  31. Zhang Y, et al.
    Mediator subunit 16 functions in the regulation of iron uptake gene expression in Arabidopsis.
    New Phytol., 2014. 203(3): p. 770-83
    [PMID:24889527]
  32. 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]
  33. Mai HJ, et al.
    Iron and FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR-dependent regulation of proteins and genes in Arabidopsis thaliana roots.
    Proteomics, 2015. 15(17): p. 3030-47
    [PMID:25951126]