RegulonDB RegulonDB 10.8: Operon Form
   

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




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


Transcription unit          
Name: fdhF
Synonym(s): OP00207
Gene(s): fdhF   Genome Browser M3D Gene expression COLOMBOS
Note(s): This transcription unit is repressed and induced anaerobically. It is repressed in the presence of nitrate and induced in the presence of formate Wang H,2003
Based on qRT-PCR, it was found that three selenopolypeptide genes, fdnG, fdoG, and fdhF, were induced more than 2-fold by both 0.01 and 5 mM Na2SeO3 (sodium selenite) 24531660
Reference(s): [1] Rosentel JK., et al., 1995
[2] Wang H., et al., 2003
Promoter
Name: fdhFp
+1: 4299407
Sigma Factor: Sigma54 Sigmulon
Distance from start of the gene: 41
Sequence: cccgtaatatcagggaatgaccccacataaaatgtggcataaaagatgcatactgtagtcGagagcgcgtatgcgtgattt
                                   -24         -12          +1                   
Evidence: [TIM]
Reference(s): [3] Birkmann A., et al., 1987
[4] Schlensog V., et al., 1994
Terminator(s)
Type: rho-independent
Sequence: tcgaatggatAAAAAAACAGCCTCCGAAAGGAGGCTGTAGAAAGgacggtatta
Reference(s): [5] Bognar AL., et al., 1987
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
nd FNR1 activator fdhFp nd nd nd nd nd [GEA] [8]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote FhlA-formate activator fdhFp 4299505 4299518 -104.5 cgtttcgtcaCGTCAAAACTGACGacagcctgtt nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [4]
remote FhlA-formate activator fdhFp 4299530 4299543 -129.5 gcgtgatggcTGTCACGCGGTATTtcgtttcgtc nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [3], [4], [6], [7]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd NarL-Phosphorylated1 repressor fdhFp nd nd nd nd nd [BPP], [GEA] [2]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd NarP-Phosphorylated1 activator fdhFp nd nd nd nd nd [GEA] [2]
Note(s): 1Under anaerobiosis, FNR activates fdhF gene expression, but it is not known if this regulation is direct or indirect Salmon K,2003.
This regulatory interaction was determined only by microarray analysis.1NarL appears to bind two regions upstream of the fdhF promoter: one of them is between position -130 and position ?175 and the other one is between position -190 and position -27 relative to the transcription start site. NarP appears to antagonize the ability of NarL to repress fdhF gene expression.1NarP appears to be a mild antagonist of NarL's ability to repress fdhF gene expresion Wang H,2003 .3Under anaerobiosis, FNR activates fdhF gene expression, but it is not known if this regulation is direct or indirect Salmon K,2003.
This regulatory interaction was determined only by microarray analysis.
4NarP appears to be a mild antagonist of NarL's ability to repress fdhF gene expresion Wang H,2003 .
5NarL appears to bind two regions upstream of the fdhF promoter: one of them is between position -130 and position ?175 and the other one is between position -190 and position -27 relative to the transcription start site. NarP appears to antagonize the ability of NarL to repress fdhF gene expression.


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Translational
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -9.8 4299382 4299412 atgcatactgTAGTCGAGAGCGCGTATGCGTGATTTGATTaactggagcg
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"
REGULATION, RNA cis-regulatory element:  
Rfam type: Cis-reg
Strand: reverse
  Description Rfam score Left Pos Right Pos Sequence (RNA-strand)
  Selenocysteine insertion sequence 2 87.1 4298900 4298954 ugcugcgcucGUGUCUGACACGGCCCAUCGGUUGCAGGUCUGCACCAAUCGGUCGGUAAUGGCGCaaugagcaau
Notes: "The provied "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appears as the reverse complement of the sequence delimited by LeftPos-RightPos"




Reference(s)    

 [1] Rosentel JK., Healy F., Maupin-Furlow JA., Lee JH., Shanmugam KT., 1995, Molybdate and regulation of mod (molybdate transport), fdhF, and hyc (formate hydrogenlyase) operons in Escherichia coli., J Bacteriol 177(17):4857-64

 [2] Wang H., Gunsalus RP., 2003, Coordinate regulation of the Escherichia coli formate dehydrogenase fdnGHI and fdhF genes in response to nitrate, nitrite, and formate: roles for NarL and NarP., J Bacteriol 185(17):5076-85

 [3] Birkmann A., Zinoni F., Sawers G., Bock A., 1987, Factors affecting transcriptional regulation of the formate-hydrogen-lyase pathway of Escherichia coli., Arch Microbiol 148(1):44-51

 [4] Schlensog V., Lutz S., Bock A., 1994, Purification and DNA-binding properties of FHLA, the transcriptional activator of the formate hydrogenlyase system from Escherichia coli., J Biol Chem 269(30):19590-6

 [5] Bognar AL., Osborne C., Shane B., 1987, Primary structure of the Escherichia coli folC gene and its folylpolyglutamate synthetase-dihydrofolate synthetase product and regulation of expression by an upstream gene., J Biol Chem 262(25):12337-43

 [6] Birkmann A., Bock A., 1989, Characterization of a cis regulatory DNA element necessary for formate induction of the formate dehydrogenase gene (fdhF) of Escherichia coli., Mol Microbiol 3(2):187-95

 [7] Schlensog V., Bock A., 1990, Identification and sequence analysis of the gene encoding the transcriptional activator of the formate hydrogenlyase system of Escherichia coli., Mol Microbiol 4(8):1319-27

 [8] Salmon K., Hung SP., Mekjian K., Baldi P., Hatfield GW., Gunsalus RP., 2003, Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNR., J Biol Chem 278(32):29837-55


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