RegulonDB RegulonDB 10.9: Operon Form
   

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




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


Transcription unit          
Name: hybOABCDEFG
Gene(s): hybG, hybF, hybE, hybD, hybC, hybB, hybA, hybO   Genome Browser M3D Gene expression COLOMBOS
Note(s): The hybOABCDEFG operon is induced under anaerobiosis and repressed by nitrate Richard DJ,1999
A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for hybB . This structure could regulate the expression of the gene, as observed for hemL gene expression 31964733.
Evidence: [IEP] Inferred from expression pattern
[ITCR] Inferred through co-regulation
[PM] Polar mutation
Reference(s): [1] Menon NK., et al., 1994
[2] Sargent F., et al., 1998
Promoter
Name: hybOp1
+1: 3146363
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 102
Sequence: attaattacactaatgcttcttcccttcgttttagcgccccgccgcagtatcatgatatcGataaccataataaatgtgtg
                          -35                    -10        +1                   
Note(s): hybOp1 was validated experimentally in anaerobic conditions Chung D,2013.
Evidence: [HIPP]
[HTTIM]
[ICWHO]
[RS-EPT-CBR]
[TIM]
Reference(s): [3] Chung D., et al., 2013
[4] Huerta AM., et al., 2003
[5] Mendoza-Vargas A., et al., 2009
[6] Richard DJ., et al., 1999
[7] Salgado H, et al., 2012
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
proximal ArcA-Phosphorylated repressor hybOp1 3146413 3146427 -57.0 tattatcttgCTTTAATTAATTACACtaatgcttct nd [APIORCISFBSCS], [GEA] [6]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal NarL-Phosphorylated repressor hybOp1 3146340 3146346 21.0 cataataaatGTGTGGTAaatggcgcat nd [APIORCISFBSCS], [GEA] [6]
proximal NarL-Phosphorylated repressor hybOp1 3146411 3146417 -51.0 ctttaattaaTTACACTAatgcttcttc nd [APIORCISFBSCS], [GEA] [6]
proximal NarL-Phosphorylated repressor hybOp1 3146436 3146442 -76.0 ttgatcaaacATACGTATtatcttgctt nd [APIORCISFBSCS], [GEA] [6]




Reference(s)    

 [1] Menon NK., Chatelus CY., Dervartanian M., Wendt JC., Shanmugam KT., Peck HD., Przybyla AE., 1994, Cloning, sequencing, and mutational analysis of the hyb operon encoding Escherichia coli hydrogenase 2., J Bacteriol 176(14):4416-23

 [2] Sargent F., Ballantine SP., Rugman PA., Palmer T., Boxer DH., 1998, Reassignment of the gene encoding the Escherichia coli hydrogenase 2 small subunit--identification of a soluble precursor of the small subunit in a hypB mutant., Eur J Biochem 255(3):746-54

 [3] Chung D., Park D., Myers K., Grass J., Kiley P., Landick R., Keles S., 2013, dPeak: high resolution identification of transcription factor binding sites from PET and SET ChIP-Seq data., PLoS Comput Biol 9(10):e1003246

 [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] Mendoza-Vargas A., Olvera L., Olvera M., Grande R., Vega-Alvarado L., Taboada B., Jimenez-Jacinto V., Salgado H., Juarez K., Contreras-Moreira B., Huerta AM., Collado-Vides J., Morett E., 2009, Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli., PLoS One 4(10):e7526

 [6] Richard DJ., Sawers G., Sargent F., McWalter L., Boxer DH., 1999, Transcriptional regulation in response to oxygen and nitrate of the operons encoding the [NiFe] hydrogenases 1 and 2 of Escherichia coli., Microbiology 145 ( Pt 10):2903-12

 [7] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.


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