RegulonDB RegulonDB 11.1: 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) Campagne S, Marsh ME, Capitani G, Vorholt JA, Allain FH,2014
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: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [3] Birkmann A., et al., 1987
[4] Huerta AM., et al., 2003
[5] Schlensog V., et al., 1994
Terminator(s)
Type: rho-independent
Sequence: tcgaatggatAAAAAAACAGCCTCCGAAAGGAGGCTGTAGAAAGgacggtatta
Reference(s): [6] Bognar AL., et al., 1987
TF binding sites (TFBSs)
[FNR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd FNR activator fdhFp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [7]
[FhlA,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote FhlA-formate activator fdhFp 4299505 4299518 -104.5 cgtttcgtcaCGTCAAAACTGACGacagcctgtt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [5]
remote FhlA-formate activator fdhFp 4299530 4299543 -129.5 gcgtgatggcTGTCACGCGGTATTtcgtttcgtc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [5]
[NarL,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd NarL-phosphorylated repressor fdhFp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2]
[NarP,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd NarP-phosphorylated activator fdhFp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [2]


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"


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins


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] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

 [5] 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

 [6] 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

 [7] 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

RegulonDB