RegulonDB RegulonDB 10.6.3: Operon Form
   

ftnA operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: ftnA
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit          
Gene(s): ftnA   Genome Browser M3D Gene expression COLOMBOS
Note(s): Fur antagonizes the H-NS effect in the ftnA promoter. Fur reverses H-NS-mediated repression of ftnA; displacement of H-NS from sites II (-130.5), III (-83), and IV (-56) prevents cooperative binding at sites V (-21) and VI (+16) and leads to derepression |CITS:[20015147]|. H-NS represses the ftnA operon through six AT-rich binding sites that oligomerize and cause DNA looping |CITS:[20015147]|. The displacement of the upstream sites of H-NS by Fur prevents cooperative H-NS binding at the downstream sites on the transcriptional start site of the ftnA promoter, which allows access to RNA polymerase |CITS:[20015147]|. This manner of activation by Fe2+-Fur through H-NS antisilencing represents a new mechanism for iron-induced gene expression. In addition, ftnA is the first example of a gene with a defined alternative Fe2+-Fur induction pathway in Escherichia coli |CITS:[20015147]|.
Hepcidin, an antimicrobial peptide, increases the expression of ftnA under conditions of iron availability, in a Fur-independent way |CITS:[29659799]|.
Evidence: [ICWHO] Inferred computationally without human oversight
[LTED] Length of transcript experimentally determined
[LTED] Length of transcript experimentally determined
Reference(s): [1] Izuhara M., et al., 1991
Promoter
Name: ftnAp
+1: 1988682
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 34
Sequence: ataattgaagtttatattttaccttttgcaaataataaaataacaaattatagtgacgccAcagcaacaaatataaccttt
                          -35                    -10        +1                   
Evidence: [HIPP]
[RS-EPT-CBR]
Reference(s): [1] Izuhara M., et al., 1991
[2] Salgado H, et al., 2012
TF binding sites (TFBSs)
[Fur,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Fur-Fe2+ activator ftnAp 1988584 1988602 -89.0 tgattaaagaAATAGCGGTAATGCGTTTTattcccattc nd [BPP], [GEA], [HIBSCS] [3]
proximal Fur-Fe2+ activator ftnAp 1988590 1988609 -83.0 aagaaatagcGGTAATGCGTTTTATTCCCAttcgtatttt nd [BPP], [GEA], [HIBSCS] [3]
proximal Fur-Fe2+ activator ftnAp 1988596 1988614 -77.0 tagcggtaatGCGTTTTATTCCCATTCGTatttttaata nd [BPP], [GEA], [HIBSCS] [3]
proximal Fur-Fe2+ activator ftnAp 1988602 1988620 -71.0 taatgcgtttTATTCCCATTCGTATTTTTaataattgaa nd [BPP], [GEA], [HIBSCS] [3]
proximal Fur-Fe2+ activator ftnAp 1988608 1988626 -65.0 gttttattccCATTCGTATTTTTAATAATtgaagtttat nd [BPP], [GEA], [HIBSCS] [3]
[H-NS,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote H-NS repressor ftnAp 1988546 1988556 -131.5 ctttctctaaATATTTTAATCagcgagggga nd [BPP], [GEA] [3]
remote H-NS repressor ftnAp 1988571 1988591 -101.5 aggggatcttCGCTGATTAAAGAAATAGCGGtaatgcgttt nd [BPP], [GEA] [3]
proximal H-NS repressor ftnAp 1988590 1988609 -83.0 aagaaatagcGGTAATGCGTTTTATTCCCAttcgtatttt nd [BPP], [GEA] [3]
proximal H-NS repressor ftnAp 1988609 1988644 -56.0 ttttattcccATTCGTATTTTTAATAATTGAAGTTTATATTTTACCttttgcaaat nd [BPP], [GEA] [3]
proximal H-NS repressor ftnAp 1988646 1988678 -20.5 tattttacctTTTGCAAATAATAAAATAACAAATTATAGTGACgccacagcaa nd [BPP], [GEA] [3]
proximal H-NS repressor ftnAp 1988687 1988707 15.5 acgccacagcAACAAATATAACCTTTGTGGAgcactatcat nd [BPP], [GEA] [3]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Translational
Strand: forward
Evidence: [ICA] Inferred by computational analysis
Reference(s): [4] null null
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -11.76 1988671 1988714 taacaaattaTAGTGACGCCACAGCAACAAATATAACCTTTGTGGAGCACTATcatgctgaaa
Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos"


Evidence    

 [HIPP] Human inference of promoter position

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

 [HIBSCS] Human inference based on similarity to consensus sequences


Reference(s)    

 [1] Izuhara M., Takamune K., Takata R., 1991, Cloning and sequencing of an Escherichia coli K12 gene which encodes a polypeptide having similarity to the human ferritin H subunit., Mol Gen Genet 225(3):510-3

 [2] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Mu¿¿iz-Rascado L, Garc¿¿a-Sotelo JS, Weiss V, Solano-Lira H, Mart¿¿nez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hern¿¿ndez S, Alquicira-Hern¿¿ndez K, L¿¿pez-Fuentes A, Porr¿¿n-Sotelo L, Huerta AM, Bonavides-Mart¿¿nez C, Balderas-Mart¿¿nez YI, Pannier L, Olvera M, Labastida A, Jim¿¿nez-Jacinto V, Vega-Alvarado L, Del Moral-Ch¿¿vez V, Hern¿¿ndez-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

 [3] Nandal A., Huggins CC., Woodhall MR., McHugh J., Rodriguez-Quinones F., Quail MA., Guest JR., Andrews SC., 2010, Induction of the ferritin gene (ftnA) of Escherichia coli by Fe(2+)-Fur is mediated by reversal of H-NS silencing and is RyhB independent., Mol Microbiol 75(3):637-57

 [4] null, null, null, null


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