RegulonDB RegulonDB 10.9: 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: [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-cAMP1 activator hyfAp 2601000 2601022 -160.5 atacctcactTCTCGTGATCAAGATCACATTCTcgctttcccc nd [AIBSCS], [APIORCISFBSCS], [GEA] [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 FNR1 repressor hyfAp 2601059 2601072 -105.5 aatccattttTTGCTGAACGTTAATgaccatcatt nd [APIORCISFBSCS], [GEA] [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-formate1 activator hyfAp 2601034 2601047 -130.0 gctttcccctGCGACACGGGTGTCGaatccatttt 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 HyfR1 activator hyfAp 2601033 2601050 -129.5 cgctttccccTGCGACACGGGTGTCGAATccattttttg nd [AIBSCS], [GEA] [3], [4]
Note(s): 1CRP and anaerobiosis are required for the hyf operon expression when the HyfR protein is the activator Self WT,2004.1It seems that Fnr repress the hyf operon expression when it is activated by HyfR. Its is possible that binding of FNR may minimize the binding of HyfR, whose binding site is only 25 bases upstream of the FNR-binding site Self WT,2004.1Only FhlA mutants can activate the transcription of the hyf operon. The HycA protein acts as an antiactivator of FhlA Skibinski DA,20021HypF activates hyf operon transcription only when it is expressed from a heterologous promoter Skibinski DA,2002. Self WT,2004.1CRP and anaerobiosis are required for the hyf operon expression when the HyfR protein is the activator Self WT,2004.
2Only FhlA mutants can activate the transcription of the hyf operon. The HycA protein acts as an antiactivator of FhlA Skibinski DA,2002
3HypF activates hyf operon transcription only when it is expressed from a heterologous promoter Skibinski DA,2002. Self WT,2004.
4It seems that Fnr repress the hyf operon expression when it is activated by HyfR. Its is possible that binding of FNR may minimize the binding of HyfR, whose binding site is only 25 bases upstream of the FNR-binding site Self WT,2004.


Evidence    

 [HIPP] Human inference of promoter position

 [ICWHO] Inferred computationally without human oversight

 [TIM] Transcription initiation mapping

 [AIBSCS] Automated inference based on similarity to consensus sequences

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

 [GEA] Gene expression analysis


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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