RegulonDB RegulonDB 10.8: Operon Form
   

fldA-uof-fur operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: fldA-uof-fur
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit          
Name: fur
Synonym(s): OP00163
Gene(s): fur   Genome Browser M3D Gene expression COLOMBOS
Note(s):
The expression of the fur gene was increased in mutants for two genes that encode two terminal oxidases, cyoA and cydB, and in mutant for the transcriptional regulator Fnr. However, it is unknown if the effects of the transcriptional regulator act directly on gene expression; also, it is unknown which of the four promoters that transcribe the gene could be regulated by the regulator Kumar R,2011
Direct activation of fur transcription by Crl is not likely, inasmuch as fur is transcribed via σ70 and Crl only transcribes genes dependent on σS Wiebe H,2015 Based on molecular analysis, an interaction between Crl and Fur proteins is suggested; both activate the expression of fur Wiebe H,2015
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] De Lorenzo V., et al., 1988
[2] Perez-Martin J., et al., 1993
[3] Schaffer S., et al., 1985
Promoter
Name: furpa
+1: 710716
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 70
Sequence: acaatatttgccagggacttgtggttttcatttaggcgtggcaattctataatgatacgcAttatctcaagagcaaattct
                           -35                  -10         +1                   
Evidence: [CV(RS-EPT-CBR)]
[CV(TIM)]
[HIPP]
[RS-EPT-CBR]
[TIM]
Reference(s): [1] De Lorenzo V., et al., 1988
[4] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: aacaaataagTGAGAGCTGTAACTCTCgcttttctta
Reference(s): [3] Schaffer S., et al., 1985
Type: rho-independent
Sequence: tgcataaaaaAGCCAACCCGCAGGTTGGCttttctcgtt
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cAMP activator furpa 710783 710804 -77.5 ttgccgttgtAAATGTAAGCTGTGCCACGTTTttattaacaa nd [APIORCISFBSCS], [SM] [1]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Fur-Fe2+ repressor furpa 710708 710726 -1.0 gcaattctatAATGATACGCATTATCTCAagagcaaatt nd [APIORCISFBSCS], [BPP] [5]
proximal Fur-Fe2+ repressor furpa 710714 710732 -7.0 ggcgtggcaaTTCTATAATGATACGCATTatctcaagag nd [APIORCISFBSCS], [BPP] [1], [5], [6]


Transcription unit          
Name: fur
Gene(s): fur   Genome Browser M3D Gene expression COLOMBOS
Note(s):
The expression of the fur gene was increased in mutants for two genes that encode two terminal oxidases, cyoA and cydB, and in mutant for the transcriptional regulator Fnr. However, it is unknown if the effects of the transcriptional regulator act directly on gene expression; also, it is unknown which of the four promoters that transcribe the gene could be regulated by the regulator Kumar R,2011
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] De Lorenzo V., et al., 1988
[2] Perez-Martin J., et al., 1993
[3] Schaffer S., et al., 1985
Promoter
Name: furpb
+1: 710723
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 77
Sequence: tttattaacaatatttgccagggacttgtggttttcatttaggcgtggcaattctataatGatacgcattatctcaagagc
                                  -35                  -10  +1                   
Evidence: [CV(RS-EPT-CBR)]
[CV(TIM)]
[HIPP]
[RS-EPT-CBR]
[TIM]
Reference(s): [1] De Lorenzo V., et al., 1988
[4] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: aacaaataagTGAGAGCTGTAACTCTCgcttttctta
Reference(s): [3] Schaffer S., et al., 1985
Type: rho-independent
Sequence: tgcataaaaaAGCCAACCCGCAGGTTGGCttttctcgtt
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cAMP activator furpb 710783 710804 -70.5 ttgccgttgtAAATGTAAGCTGTGCCACGTTTttattaacaa nd [APIORCISFBSCS], [SM] [1]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Fur-Fe2+ repressor furpb 710708 710726 7.0 gcaattctatAATGATACGCATTATCTCAagagcaaatt nd [APIORCISFBSCS], [BPP] [5]
proximal Fur-Fe2+ repressor furpb 710714 710732 1.0 ggcgtggcaaTTCTATAATGATACGCATTatctcaagag nd [APIORCISFBSCS], [BPP] [1], [5], [6]


Transcription unit          
Name: uof-fur
Gene(s): fur, uof   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [2] Perez-Martin J., et al., 1993
[3] Schaffer S., et al., 1985
[7] Zheng M., et al., 1999
Promoter
Name: uofp
+1: 710829
Distance from start of the gene: 104
Sequence: gccaatcaaaataattgctacaaatttgtaacttttgctgttgtacctgtacaatgtcccGgtgttcaagtggccttgccg
Evidence: [TIM]
Reference(s): [7] Zheng M., et al., 1999
Terminator(s)
Type: rho-independent
Sequence: aacaaataagTGAGAGCTGTAACTCTCgcttttctta
Reference(s): [3] Schaffer S., et al., 1985
Type: rho-independent
Sequence: tgcataaaaaAGCCAACCCGCAGGTTGGCttttctcgtt
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal OxyR activator uofp 710861 710877 -40.0 caatcaaaatAATTGCTACAAATTTGTaacttttgct nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [7]
proximal OxyR2 activator uofp 710883 710899 -62.0 acgccgtattAATAGATAATGCCAATCaaaataattg nd [APIORCISFBSCS], [BPP], , [CV(GEA)], [CV(GEA)], [GEA], [IHBCE], [7], [8]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal SoxS activator uofp 710881 710900 -61.5 tacgccgtatTAATAGATAATGCCAATCAAaataattgct nd [BPP], , [IHBCE], [7], [8]
Note(s): 2Induction of fur by OxyR is necessary to keep
the Fur regulon repressed under H2O2 stress 174620261Induction of fur by OxyR is necessary to keep
the Fur regulon repressed under H2O2 stress 17462026


Transcription unit          
Name: fldA-uof-fur
Synonym(s): fldA-fur
Gene(s): fur, uof, fldA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [7] Zheng M., et al., 1999
Promoter
Name: fldAp
+1: 711521
Distance from start of the gene: 56
Sequence: tgtgcagtcctgctcgtttgctgattccgcaagactgcctgttctgctatgattgcctttAtccgtgggcaattttccacc
Evidence: [TIM]
Reference(s): [7] Zheng M., et al., 1999
Terminator(s)
Type: rho-independent
Sequence: aacaaataagTGAGAGCTGTAACTCTCgcttttctta
Reference(s): [3] Schaffer S., et al., 1985
Type: rho-independent
Sequence: tgcataaaaaAGCCAACCCGCAGGTTGGCttttctcgtt
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal SoxS activator fldAp 711573 711592 -61.5 ttccactttcATGTAGCACAGTGTGCAGTCctgctcgttt nd [APIORCISFBSCS], [BPP], , [CV(GEA)], [CV(GEA)], [GEA], [IHBCE], [7], [8], [9], [10]


Regulation by sRNA    
  Small RNA name (Regulator) Regulation type Mechanism Function Binding Sites Evidence Reference
LeftPos RightPos Sequence (RNA-strand)
  ryhB antisense post-transcriptional regulation repressor       [IMP] [11]
Notes: "The provided sequence is that of the RNA strand,i.e. 'U's are showed instead the 'T'"




Reference(s)    

 [1] De Lorenzo V., Herrero M., Giovannini F., Neilands JB., 1988, Fur (ferric uptake regulation) protein and CAP (catabolite-activator protein) modulate transcription of fur gene in Escherichia coli., Eur J Biochem 173(3):537-46

 [2] Perez-Martin J., Espinosa M., 1993, Protein-induced bending as a transcriptional switch., Science 260(5109):805-7

 [3] Schaffer S., Hantke K., Braun V., 1985, Nucleotide sequence of the iron regulatory gene fur., Mol Gen Genet 200(1):110-3

 [4] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-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.

 [5] Chen Z., Lewis KA., Shultzaberger RK., Lyakhov IG., Zheng M., Doan B., Storz G., Schneider TD., 2007, Discovery of Fur binding site clusters in Escherichia coli by information theory models., Nucleic Acids Res 35(20):6762-77

 [6] Newman DL., Shapiro JA., 1999, Differential fiu-lacZ fusion regulation linked to Escherichia coli colony development., Mol Microbiol 33(1):18-32

 [7] Zheng M., Doan B., Schneider TD., Storz G., 1999, OxyR and SoxRS regulation of fur., J Bacteriol 181(15):4639-43

 [8] Seo SW., Kim D., Szubin R., Palsson BO., 2015, Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655., Cell Rep 12(8):1289-99

 [9] Martin RG., Gillette WK., Rhee S., Rosner JL., 1999, Structural requirements for marbox function in transcriptional activation of mar/sox/rob regulon promoters in Escherichia coli: sequence, orientation and spatial relationship to the core promoter., Mol Microbiol 34(3):431-41

 [10] Pomposiello PJ., Bennik MH., Demple B., 2001, Genome-wide transcriptional profiling of the Escherichia coli responses to superoxide stress and sodium salicylate., J Bacteriol 183(13):3890-902

 [11] Vecerek B., Moll I., Blasi U., 2007, Control of Fur synthesis by the non-coding RNA RyhB and iron-responsive decoding., EMBO J 26(4):965-75


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