RegulonDB RegulonDB 10.10: Operon Form
   

hyfABCDEFGHIJR-focB operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: hyfABCDEFGHIJR-focB
Gene(s): hyfA, hyfB, hyfC, hyfD, hyfE, hyfF, hyfG, hyfH, hyfI, hyfJ, hyfR, focB   Genome Browser M3D Gene expression COLOMBOS
Note(s): This operon is apparently silent, because it was not expressed at a significant level in a wild-type strain under the tested conditions Andrews SC,1997.
Evidence: [BTEI] Boundaries of transcription experimentally identified
[IEP] Inferred from expression pattern
[ITCR] Inferred through co-regulation
Reference(s): [1] Andrews SC., et al., 1997
Promoter
Name: hyfAp
+1: 2601171
Sigma Factor: Sigma54 Sigmulon
Distance from start of the gene: 30
Sequence: cataacttattgaatatattgagttaatcagaatggcatcctttatgcaatatgaaatgcAatgtttcatatcattttcaa
                                  -24         -12           +1                   
Evidence: [APIORCISFBSCS]
[HIPP]
[ICWHO]
[TIM]
Reference(s): [2] Huerta AM., et al., 2003
[3] Skibinski DA., et al., 2002
TF binding sites (TFBSs)
[CRP,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote CRP-cyclic-AMP activator hyfAp 2601000 2601022 -160.5 atacctcactTCTCGTGATCAAGATCACATTCTcgctttcccc nd [GEA], [AIBSCS], [APIORCISFBSCS] [4], [5]
[FNR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote FNR repressor hyfAp 2601059 2601072 -105.5 aatccattttTTGCTGAACGTTAAtgaccatcat nd [GEA], [APIORCISFBSCS] [4]
[FhlA,+] Phrase
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 hyfAp 2601034 2601047 -130.0 gctttcccctGCGACACGGGTGTCgaatccattt nd [GEA] [3], [4]
[HyfR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote HyfR activator hyfAp 2601033 2601050 -129.5 cgctttccccTGCGACACGGGTGTCGAAtccatttttt nd [GEA], [AIBSCS] [3], [4]


Evidence    

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

 [HIPP] Human inference of promoter position

 [ICWHO] Inferred computationally without human oversight

 [TIM] Transcription initiation mapping

 [GEA] Gene expression analysis

 [AIBSCS] Automated inference based on similarity to consensus sequences


Reference(s)    

 [1] Andrews SC., Berks BC., McClay J., Ambler A., Quail MA., Golby P., Guest JR., 1997, A 12-cistron Escherichia coli operon (hyf) encoding a putative proton-translocating formate hydrogenlyase system., Microbiology 143 ( Pt 11):3633-47

 [2] 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

 [3] Skibinski DA., Golby P., Chang YS., Sargent F., Hoffman R., Harper R., Guest JR., Attwood MM., Berks BC., Andrews SC., 2002, Regulation of the hydrogenase-4 operon of Escherichia coli by the sigma(54)-dependent transcriptional activators FhlA and HyfR., J Bacteriol 184(23):6642-53

 [4] Self WT., Hasona A., Shanmugam KT., 2004, Expression and regulation of a silent operon, hyf, coding for hydrogenase 4 isoenzyme in Escherichia coli., J Bacteriol 186(2):580-7

 [5] Tsai MJ., Wang JR., Yang CD., Kao KC., Huang WL., Huang HY., Tseng CP., Huang HD., Ho SY., 2018, PredCRP: predicting and analysing the regulatory roles of CRP from its binding sites in Escherichia coli., Sci Rep 8(1):951

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