RegulonDB RegulonDB 11.1: Operon Form
   

hcp-hcr-poxB-ltaE-ybjT operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: hcp-hcr-poxB-ltaE-ybjT
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit       
Name: ltaE-ybjT
Gene(s): ybjT, ltaE   Genome Browser M3D Gene expression COLOMBOS
Evidence: [IC] Inferred by curator
Promoter
Name: ltaEp
+1: 909320
Distance from start of the gene: 26
Sequence: gacgcggtgatgaagtgatcgaactggcgaaaacaaactggctaaggtaaaaagggtggcAtttcccgtcataataaggac
Evidence: [EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP]
[RS-EPT-CBR]
Reference(s): [1] Mendoza-Vargas A., et al., 2009
[2] Salgado H, et al., 2012


Transcription unit          
Name: poxB
Gene(s): poxB   Genome Browser M3D Gene expression COLOMBOS
Note(s): The poxB expression is reduced when the cell is grown on acetate, pyruvate, or glycerol El-Mansi M, Phue JN, Shiloach J,2021.
Evidence: [EXP-IEP] Inferred from expression pattern
Reference(s): [3] Chang YY., et al., 1994
Promoter
Name: poxBp1
+1: 911076
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 27
Sequence: ttagtgcctcctttctctcccatcccttccccctccgtcagatgaactaaacttgttaccGttatcacattcaggagatgg
                                -35                  -10    +1                   
Evidence: [COMP-AINF]
[COMP-HINF]
[EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [3] Chang YY., et al., 1994
[4] Huerta AM., et al., 2003
[5] Olvera L., et al., 2009
[2] Salgado H, et al., 2012
[6] Wise A., et al., 1996
TF binding sites (TFBSs)
[Cra,+] 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
nd Cra activator poxBp1 nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [8]
[MarA,+] 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 MarA activator poxBp1 911127 911146 -60.5 ttcatcgggcTATTTAACCGTTAGTGCCTCctttctctcc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [7]
[SoxS,+] 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 SoxS activator poxBp1 911127 911146 -60.5 ttcatcgggcTATTTAACCGTTAGTGCCTCctttctctcc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [7]


Transcription unit          
Name: poxB
Gene(s): poxB   Genome Browser M3D Gene expression COLOMBOS
Note(s): The poxB expression is reduced when the cell is grown on acetate, pyruvate, or glycerol El-Mansi M, Phue JN, Shiloach J,2021.
Evidence: [EXP-IEP] Inferred from expression pattern
Reference(s): [3] Chang YY., et al., 1994
Promoter
Name: poxBp2
+1: 911076
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 27
Sequence: ttagtgcctcctttctctcccatcccttccccctccgtcagatgaactaaacttgttaccGttatcacattcaggagatgg
                            -35                      -10    +1                   
Evidence: [COMP-AINF]
[COMP-HINF]
[EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [3] Chang YY., et al., 1994
[4] Huerta AM., et al., 2003
[5] Olvera L., et al., 2009
[2] Salgado H, et al., 2012
[6] Wise A., et al., 1996
TF binding sites (TFBSs)
[Cra,+] 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
nd Cra activator poxBp2 nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [8]
[MarA,+] 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 MarA activator poxBp2 911127 911146 -60.5 ttcatcgggcTATTTAACCGTTAGTGCCTCctttctctcc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [7]
[SoxS,+] 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 SoxS activator poxBp2 911127 911146 -60.5 ttcatcgggcTATTTAACCGTTAGTGCCTCctttctctcc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [7]


Transcription unit          
Name: hcp-hcr-poxB
Gene(s): poxB, hcr, hcp   Genome Browser M3D Gene expression COLOMBOS
Note(s): Based on transcriptome analysis and findings with an nrsR mutant, poxB was identified as an NsrR target due to readthrough transcription from the hcp-hcr genes Chhabra S,2015
Evidence: [EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s): [9] Chhabra S., et al., 2015
Promoter
Name: hcpp1
+1: 913845
Distance from start of the gene: 31
Sequence:
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [10] Filenko NA., et al., 2005
TF binding sites (TFBSs)
[FNR,+] 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 FNR activator hcpp1 913911 913924 -72.5 gccgccaaaaTTGCGCTAAATCAAtctcccttaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [10], [11]
[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
remote NarL-phosphorylated activator hcpp1 913942 913948 -100.0 atacctctctGGCGGTAgatccctgcc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [10], [11]
remote NarL-phosphorylated activator hcpp1 913951 913957 -109.0 ctctgcgtaaTACCTCTctggcggtag nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [10], [11]
[NarP,+] 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
remote NarP-phosphorylated activator hcpp1 913937 913952 -100.0 cgtaatacctCTCTGGCGGTAGATCCctgccgccaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [10]
remote NarP-phosphorylated activator hcpp1 913946 913961 -109.0 ttttctctgcGTAATACCTCTCTGGCggtagatccc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [10]
[NsrR,-] 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 NsrR repressor hcpp1 913831 913849 6.0 taaccttaaaCATGTATATTAAATATAACtttaaaaggt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IMP-SITE-MUTATION] C [11], [12], [13]
[OxyR,+] 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
nd OxyR activator hcpp1 nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [14]


Transcription unit          
Name: hcp-hcr
Gene(s): hcr, hcp   Genome Browser M3D Gene expression COLOMBOS
Note(s): The expression of hcp-hcr is induced by nitrite and nitrate, and this induction is mediated by NarP and NarL van den Berg WA,2000. Vine CE,2011 and by nitrosative stress mediated by OxyR Seth D,2012.
Evidence: [EXP-IMP-POLAR-MUTATION] Polar mutation
Reference(s): [15] van den Berg WA., et al., 2000
Promoter
Name: hcpp1
+1: 913845
Distance from start of the gene: 31
Sequence:
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [10] Filenko NA., et al., 2005
TF binding sites (TFBSs)
[FNR,+] 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 FNR activator hcpp1 913911 913924 -72.5 gccgccaaaaTTGCGCTAAATCAAtctcccttaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [10], [11]
[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
remote NarL-phosphorylated activator hcpp1 913942 913948 -100.0 atacctctctGGCGGTAgatccctgcc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [10], [11]
remote NarL-phosphorylated activator hcpp1 913951 913957 -109.0 ctctgcgtaaTACCTCTctggcggtag nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [10], [11]
[NarP,+] 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
remote NarP-phosphorylated activator hcpp1 913937 913952 -100.0 cgtaatacctCTCTGGCGGTAGATCCctgccgccaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [10]
remote NarP-phosphorylated activator hcpp1 913946 913961 -109.0 ttttctctgcGTAATACCTCTCTGGCggtagatccc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [10]
[NsrR,-] 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 NsrR repressor hcpp1 913831 913849 6.0 taaccttaaaCATGTATATTAAATATAACtttaaaaggt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IMP-SITE-MUTATION] C [11], [12], [13]
[OxyR,+] 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
nd OxyR activator hcpp1 nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [14]


Transcription unit       
Name: hcp-hcr
Gene(s): hcr, hcp   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IEP-COREGULATION] Inferred through co-regulation
[EXP-IMP-POLAR-MUTATION] Polar mutation
Reference(s): [16] Rhodius VA., et al., 2005
[15] van den Berg WA., et al., 2000
Promoter
Name: hcpp2
+1: 914129
Sigma Factor: Sigma24 Sigmulon
Distance from start of the gene: 315
Sequence: cgcggcgttttttaatgatctggcccgtgaactgattgctattatgttgatccctgggctGattcgccgcagccgctctac
                            -35                   -10       +1                   
Evidence: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
[COMP-AINF-SIMILAR-TO-CONSENSUS]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [4] Huerta AM., et al., 2003
[16] Rhodius VA., et al., 2005


Transcription unit       
Name: poxB-ltaE-ybjT
Gene(s): ybjT, ltaE, poxB   Genome Browser M3D Gene expression COLOMBOS
Evidence: [COMP-AINF] Inferred computationally without human oversight


Evidence    

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

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

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-HINF] Inferred by a human based on computational evidence

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

 [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.

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins

 [EXP-IMP-SITE-MUTATION] Site mutation

 [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] Binding of cellular extracts

 [COMP-AINF-POSITIONAL-IDENTIFICATION] Automated inference of promoter position

 [COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences


Reference(s)    

 [1] 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

 [2] 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.

 [3] Chang YY., Wang AY., Cronan JE., 1994, Expression of Escherichia coli pyruvate oxidase (PoxB) depends on the sigma factor encoded by the rpoS(katF) gene., Mol Microbiol 11(6):1019-28

 [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] Olvera L., Mendoza-Vargas A., Flores N., Olvera M., Sigala JC., Gosset G., Morett E., Bolivar F., 2009, Transcription analysis of central metabolism genes in Escherichia coli. Possible roles of sigma38 in their expression, as a response to carbon limitation., PLoS One 4(10):e7466

 [6] Wise A., Brems R., Ramakrishnan V., Villarejo M., 1996, Sequences in the -35 region of Escherichia coli rpoS-dependent genes promote transcription by E sigma S., J Bacteriol 178(10):2785-93

 [7] Martin RG., Gillette WK., Rhee S., Rosner JL., 1999, Structural requirements for marbox function in transcriptional activation of mar/sox/rob regulon promoters in Escherichia coli: sequence, orientation and spatial relationship to the core promoter., Mol Microbiol 34(3):431-41

 [8] Son YJ., Phue JN., Trinh LB., Lee SJ., Shiloach J., 2011, The role of Cra in regulating acetate excretion and osmotic tolerance in E. coli K-12 and E. coli B at high density growth., Microb Cell Fact 10:52

 [9] Chhabra S., Spiro S., 2015, Inefficient translation of nsrR constrains behaviour of the NsrR regulon in Escherichia coli., Microbiology 161(10):2029-38

 [10] Filenko NA., Browning DF., Cole JA., 2005, Transcriptional regulation of a hybrid cluster (prismane) protein., Biochem Soc Trans 33(Pt 1):195-7

 [11] Filenko N., Spiro S., Browning DF., Squire D., Overton TW., Cole J., Constantinidou C., 2007, The NsrR regulon of Escherichia coli K-12 includes genes encoding the hybrid cluster protein and the periplasmic, respiratory nitrite reductase., J Bacteriol 189(12):4410-7

 [12] Chismon DL., Browning DF., Farrant GK., Busby SJ., 2010, Unusual organization, complexity and redundancy at the Escherichia coli hcp-hcr operon promoter., Biochem J 430(1):61-8

 [13] Partridge JD., Bodenmiller DM., Humphrys MS., Spiro S., 2009, NsrR targets in the Escherichia coli genome: new insights into DNA sequence requirements for binding and a role for NsrR in the regulation of motility., Mol Microbiol 73(4):680-94

 [14] Seth D., Hausladen A., Wang YJ., Stamler JS., 2012, Endogenous protein S-Nitrosylation in E. coli: regulation by OxyR., Science 336(6080):470-3

 [15] van den Berg WA., Hagen WR., van Dongen WM., 2000, The hybrid-cluster protein ('prismane protein') from Escherichia coli. Characterization of the hybrid-cluster protein, redox properties of the [2Fe-2S] and [4Fe-2S-2O] clusters and identification of an associated NADH oxidoreductase containing FAD and [2Fe-2S]., Eur J Biochem 267(3):666-76

 [16] Rhodius VA., Suh WC., Nonaka G., West J., Gross CA., 2005, Conserved and variable functions of the sigmaE stress response in related genomes., PLoS Biol 4(1):e2

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