RegulonDB RegulonDB 11.2: 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 Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020.
Evidence: [EXP-IEP] Inferred from expression pattern
[EXP-IEP-COREGULATION] Inferred through co-regulation
[EXP-IMP-POLAR-MUTATION] 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: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
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)
[ArcA,-] 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
proximal ArcA-phosphorylated repressor hybOp1 3146413 3146427 -57.0 attatcttgcTTTAATTAATTACACtaatgcttct nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [6]
[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
proximal NarL-phosphorylated repressor hybOp1 3146340 3146346 21.0 ataataaatgTGTGGTAaatggcgcat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [6]
proximal NarL-phosphorylated repressor hybOp1 3146411 3146417 -51.0 tttaattaatTACACTAatgcttcttc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [6]
proximal NarL-phosphorylated repressor hybOp1 3146436 3146442 -76.0 tgatcaaacaTACGTATtatcttgctt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [6]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-HINF-POSITIONAL-IDENTIFICATION] Human inference of promoter position

 [EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP] High-throughput transcription initiation mapping

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

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

 [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.


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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