RegulonDB RegulonDB 11.1: Operon Form
   

ompR-envZ operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: ompR-envZ
Gene(s): envZ, ompR   Genome Browser M3D Gene expression COLOMBOS
Note(s): The expression of the ompR-envZ operon is affected by antibiotic pressure. An increase in the expression of this operon is maintained during exposure to increasing concentrations of tetracycline Viveiros M, Dupont M, Rodrigues L, Couto I, Davin-Regli A, Martins M, Pagès JM, Amaral L,2007
The expression of this operon is increased by PhoB under acidic growth conditions Marzan LW,2013 but it is not known which promoter, of four transcribing the operon, is affected by PhoB.
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Comeau DE., et al., 1985
[2] Matsuyama S., et al., 1986
[3] Mizuno T., et al., 1987
Promoter
Name: ompRp3
+1: 3536639
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 55
Sequence: atatgctttgtaacaatttaggctgaaattcataccagatttagctggtgacgaacgtgaGcttttttaagaatacacgct
                                  -35                     -1+1                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [4] Huang L., et al., 1992
[5] Huerta AM., et al., 2003
Terminator(s)
Type: rho-independent
Sequence: tatccagtatCTTATAGAAAGCAAAACGGGAGGCACCTTCGCCTCCCGTTTATTTACCCTTCTTTtgtcgtgccc
Reference(s): [6] Feng CQ., et al., 2019
[7] Lesnik EA., et al., 2001
TF binding sites (TFBSs)
[CRP,+] 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 CRP-cyclic-AMP activator ompRp3 3536749 3536770 -121.0 cgcacattggGTATAACGTGATCATATCAACAgaatcaataa nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [4]


Transcription unit          
Name: ompR-envZ
Synonym(s): OP00246, ompB
Gene(s): envZ, ompR   Genome Browser M3D Gene expression COLOMBOS
Note(s): The expression of the ompR-envZ operon is affected by antibiotic pressure. An increase in the expression of this operon is maintained during exposure to increasing concentrations of tetracycline Viveiros M, Dupont M, Rodrigues L, Couto I, Davin-Regli A, Martins M, Pagès JM, Amaral L,2007
The expression of this operon is increased by PhoB under acidic growth conditions Marzan LW,2013 but it is not known which promoter, of four transcribing the operon, is affected by PhoB.
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Comeau DE., et al., 1985
[2] Matsuyama S., et al., 1986
[3] Mizuno T., et al., 1987
Promoter
Name: ompRp2
+1: 3536685
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 101
Sequence: tcaataatgtttcgccgaataaattgtatacttaagctgctgtttaatatgctttgtaacAatttaggctgaaattcatac
                             -35                  -10       +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [4] Huang L., et al., 1992
[5] Huerta AM., et al., 2003
[8] Salgado H, et al., 2012
[9] Tsui P., et al., 1991
Terminator(s)
Type: rho-independent
Sequence: tatccagtatCTTATAGAAAGCAAAACGGGAGGCACCTTCGCCTCCCGTTTATTTACCCTTCTTTtgtcgtgccc
Reference(s): [6] Feng CQ., et al., 2019
[7] Lesnik EA., et al., 2001
TF binding sites (TFBSs)
[CRP,+] 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 CRP-cyclic-AMP activator ompRp2 3536749 3536770 -75.0 cgcacattggGTATAACGTGATCATATCAACAgaatcaataa nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [4]


Transcription unit          
Name: ompR-envZ
Gene(s): envZ, ompR   Genome Browser M3D Gene expression COLOMBOS
Note(s): The expression of the ompR-envZ operon is affected by antibiotic pressure. An increase in the expression of this operon is maintained during exposure to increasing concentrations of tetracycline Viveiros M, Dupont M, Rodrigues L, Couto I, Davin-Regli A, Martins M, Pagès JM, Amaral L,2007
The expression of this operon is increased by PhoB under acidic growth conditions Marzan LW,2013 but it is not known which promoter, of four transcribing the operon, is affected by PhoB.
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Comeau DE., et al., 1985
[2] Matsuyama S., et al., 1986
[3] Mizuno T., et al., 1987
Promoter
Name: ompRp1
+1: 3536707
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 123
Sequence: taacgtgatcatatcaacagaatcaataatgtttcgccgaataaattgtatacttaagctGctgtttaatatgctttgtaa
                           -35                        -10   +1                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [4] Huang L., et al., 1992
[5] Huerta AM., et al., 2003
[9] Tsui P., et al., 1991
Terminator(s)
Type: rho-independent
Sequence: tatccagtatCTTATAGAAAGCAAAACGGGAGGCACCTTCGCCTCCCGTTTATTTACCCTTCTTTtgtcgtgccc
Reference(s): [6] Feng CQ., et al., 2019
[7] Lesnik EA., et al., 2001
TF binding sites (TFBSs)
[CRP,-] 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 CRP-cyclic-AMP repressor ompRp1 3536749 3536770 -53.0 cgcacattggGTATAACGTGATCATATCAACAgaatcaataa nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [4]
[IHF,-] 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 IHF repressor ompRp1 3536694 3536706 8.0 acttaagctgCTGTTTAATATGCtttgtaacaa nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [9]
proximal IHF repressor ompRp1 3536738 3536750 -37.0 atcatatcaaCAGAATCAATAATgtttcgccga nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [9]
remote IHF repressor ompRp1 3536803 3536815 -102.0 aggggcgtttTCATCTCGTTGATtccctttgtc nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [9]


Transcription unit          
Name: ompR-envZ
Gene(s): envZ, ompR   Genome Browser M3D Gene expression COLOMBOS
Note(s): The expression of the ompR-envZ operon is affected by antibiotic pressure. An increase in the expression of this operon is maintained during exposure to increasing concentrations of tetracycline Viveiros M, Dupont M, Rodrigues L, Couto I, Davin-Regli A, Martins M, Pagès JM, Amaral L,2007
The expression of this operon is increased by PhoB under acidic growth conditions Marzan LW,2013 but it is not known which promoter, of four transcribing the operon, is affected by PhoB.
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Comeau DE., et al., 1985
[2] Matsuyama S., et al., 1986
[3] Mizuno T., et al., 1987
Promoter
Name: ompRp4
+1: 3536755
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 171
Sequence: tcatctcgttgattccctttgtctgtttgataatgcgcacattgggtataacgtgatcatAtcaacagaatcaataatgtt
                                -35                   -10   +1                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [4] Huang L., et al., 1992
[5] Huerta AM., et al., 2003
Terminator(s)
Type: rho-independent
Sequence: tatccagtatCTTATAGAAAGCAAAACGGGAGGCACCTTCGCCTCCCGTTTATTTACCCTTCTTTtgtcgtgccc
Reference(s): [6] Feng CQ., et al., 2019
[7] Lesnik EA., et al., 2001
TF binding sites (TFBSs)
[CRP,-] 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 CRP-cyclic-AMP repressor ompRp4 3536749 3536770 -5.0 cgcacattggGTATAACGTGATCATATCAACAgaatcaataa nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [4]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

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

 [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

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


Reference(s)    

 [1] Comeau DE., Ikenaka K., Tsung KL., Inouye M., 1985, Primary characterization of the protein products of the Escherichia coli ompB locus: structure and regulation of synthesis of the OmpR and EnvZ proteins., J Bacteriol 164(2):578-84

 [2] Matsuyama S., Mizuno T., Mizushima S., 1986, Interaction between two regulatory proteins in osmoregulatory expression of ompF and ompC genes in Escherichia coli: a novel ompR mutation suppresses pleiotropic defects caused by an envZ mutation., J Bacteriol 168(3):1309-14

 [3] Mizuno T., Mizushima S., 1987, Isolation and characterization of deletion mutants of ompR and envZ, regulatory genes for expression of the outer membrane proteins OmpC and OmpF in Escherichia coli., J Biochem 101(2):387-96

 [4] Huang L., Tsui P., Freundlich M., 1992, Positive and negative control of ompB transcription in Escherichia coli by cyclic AMP and the cyclic AMP receptor protein., J Bacteriol 174(3):664-70

 [5] 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

 [6] Feng CQ., Zhang ZY., Zhu XJ., Lin Y., Chen W., Tang H., Lin H., 2019, iTerm-PseKNC: a sequence-based tool for predicting bacterial transcriptional terminators., Bioinformatics 35(9):1469-1477

 [7] Lesnik EA., Sampath R., Levene HB., Henderson TJ., McNeil JA., Ecker DJ., 2001, Prediction of rho-independent transcriptional terminators in Escherichia coli., Nucleic Acids Res 29(17):3583-94

 [8] 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.

 [9] Tsui P., Huang L., Freundlich M., 1991, Integration host factor binds specifically to multiple sites in the ompB promoter of Escherichia coli and inhibits transcription., J Bacteriol 173(18):5800-7

 [10] Guillier M., Gottesman S., 2008, The 5' end of two redundant sRNAs is involved in the regulation of multiple targets, including their own regulator., Nucleic Acids Res 36(21):6781-94

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