RegulonDB RegulonDB 10.10: Operon Form
   

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




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


Transcription unit          
Name: fhuF
Gene(s): fhuF   Genome Browser M3D Gene expression COLOMBOS
Evidence: [AISGDTU] Automated inference that a single-gene directon is a transcription unit
Promoter
Name: fhuFp1
+1: 4605694
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 31
Sequence: ttatcatttgcaagccagataaatcccttgctatcgggtaaacctatcgctatgattagcAatcattatcatttagattac
                            -35                    -10      +1                   
Evidence: [HTTIM]
[ICWHO]
[IHBCE]
[TIM]
Reference(s): [1] Huerta AM., et al., 2003
[2] Maciag A., et al., 2011
[3] Zheng M., et al., 2001
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+ repressor fhuFp1 4605741 4605759 -56.0 atcatatgatAATTTTTATCATTTGCAAGccagataaat nd [GEA], [AIBSCS], [BPP] [4], [5], [6], [7], [8]
proximal Fur-Fe2+ repressor fhuFp1 4605747 4605765 -62.0 accaatatcaTATGATAATTTTTATCATTtgcaagccag nd [GEA], [AIBSCS], [APIORCISFBSCS], [BPP] [4], [5], [6], [7], [8]
proximal Fur-Fe2+ repressor fhuFp1 4605764 4605782 -79.0 tttcattgatAATGATAACCAATATCATAtgataatttt nd [GEA], [AIBSCS], [APIORCISFBSCS], [BPP] [4], [5], [6], [7], [8]
proximal Fur-Fe2+ repressor fhuFp1 4605770 4605788 -85.0 catctctttcATTGATAATGATAACCAATatcatatgat nd [GEA], [AIBSCS], [BPP] [4], [5], [6], [7], [8]
[OxyR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal OxyR repressor fhuFp1 4605685 4605701 2.0 ctatcgctatGATTAGCAATCATTATCatttagatta [GEA], [RSE], [APIORCISFBSCS], [BPP], [CEEUMA], [IHBCE] [3], [9]
proximal OxyR repressor fhuFp1 4605707 4605723 -21.0 aatcccttgcTATCGGGTAAACCTATCgctatgatta [RSE], [CEEUMA], [IHBCE] [3], [9]
proximal OxyR repressor fhuFp1 4605769 4605785 -83.0 ctctttcattGATAATGATAACCAATAtcatatgata [GEA], [APIORCISFBSCS], [BPP] [3]
remote OxyR repressor fhuFp1 4605791 4605807 -105.0 gtacgttgcaACATGATTTCATCTCTTtcattgataa [GEA], [APIORCISFBSCS], [BPP] [3]


Transcription unit       
Name: fhuF
Gene(s): fhuF   Genome Browser M3D Gene expression COLOMBOS
Evidence: [AISGDTU] Automated inference that a single-gene directon is a transcription unit
Promoter
Name: fhuFp2
+1: 4605752
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 89
Sequence: ttgcaacatgatttcatctctttcattgataatgataaccaatatcatatgataatttttAtcatttgcaagccagataaa
                          -35                   -10         +1                   
Evidence: [HIPP]
[ICWHO]
[IHBCE]
Reference(s): [1] Huerta AM., et al., 2003
[7] Vassinova N., et al., 2000


Evidence    

 [HTTIM] High-throughput transcription initiation mapping

 [ICWHO] Inferred computationally without human oversight

 [IHBCE] Inferred by a human based on computational evidence

 [TIM] Transcription initiation mapping

 [GEA] Gene expression analysis

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [BPP] Binding of purified proteins

 [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [RSE] RNA-seq evidence

 [CEEUMA] ChIP-exo evidence used in manual assertion

 [HIPP] Human inference of promoter position


Reference(s)    

 [1] 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

 [2] Maciag A., Peano C., Pietrelli A., Egli T., De Bellis G., Landini P., 2011, In vitro transcription profiling of the σS subunit of bacterial RNA polymerase: re-definition of the σS regulon and identification of σS-specific promoter sequence elements., Nucleic Acids Res 39(13):5338-55

 [3] Zheng M., Wang X., Doan B., Lewis KA., Schneider TD., Storz G., 2001, Computation-directed identification of OxyR DNA binding sites in Escherichia coli., J Bacteriol 183(15):4571-9

 [4] 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

 [5] D'Autreaux B., Touati D., Bersch B., Latour JM., Michaud-Soret I., 2002, Direct inhibition by nitric oxide of the transcriptional ferric uptake regulation protein via nitrosylation of the iron., Proc Natl Acad Sci U S A 99(26):16619-24

 [6] Gerken H., Vuong P., Soparkar K., Misra R., 2020, Roles of the EnvZ/OmpR Two-Component System and Porins in Iron Acquisition in Escherichia coli., mBio 11(3)

 [7] Vassinova N., Kozyrev D., 2000, A method for direct cloning of fur-regulated genes: identification of seven new fur-regulated loci in Escherichia coli., Microbiology 146 Pt 12:3171-3182

 [8] Zhang F., Li B., Dong H., Chen M., Yao S., Li J., Zhang H., Liu X., Wang H., Song N., Zhang K., Du N., Xu S., Gu L., 2020, YdiV regulates Escherichia coli ferric uptake by manipulating the DNA-binding ability of Fur in a SlyD-dependent manner., Nucleic Acids Res 48(17):9571-9588

 [9] 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

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