RegulonDB RegulonDB 10.8: Operon Form
   

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




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


Transcription unit          
Name: ompF
Synonym(s): OP00066
Gene(s): ompF   Genome Browser M3D Gene expression COLOMBOS
Note(s): It was proved in an experiment with increasing concentrations of the antibiotic tetracycline that the ompC gene is induced in low concentrations (1.5 and 4 mg/L), but not in high ones (10 mg/L) 17426813 This result might be attributed to the constant increase during the experiment of micF gene expression, whose sRNA product negatively regulates the expression of the ompF gene 17426813.
MarA and Rob independently regulate expression of the outer membrane porin F gene, ompF, in response to salicylate, activating micF gene expression in response to salicylate 21398557. In addition, MarA can also repress OmpF expression through a MicF-independent pathway 21398557. On the other hand, reduction in ompC expression in a tolC mutant was due primarily to Rob 21398557.
The expression of the gene ompF is increased under acidic growth conditions in either aerobiosis or microaerobiosis Marzan LW,2013 The increased expression under aerobiosis appears to be caused by the transcription factor PhoB Marzan LW,2013
Under NlpE outer membrane lipoprotein overexpression, the transcription of the ompF gene is decreased by CpxR Raivio TL,2013
Reference(s): [1] Mizuno T., et al., 1983
Promoter
Name: ompFp
+1: 987092
Sigma Factor: Sigma38, Sigma70
Distance from start of the gene: 110
Sequence: ctttatctttgtagcactttcacggtagcgaaacgttagtttgaatggaaagatgcctgcAgacacataaagacaccaaac
                         -35                     -10        +1                   
Note(s): Porin regulation by the CpxA-CpxR system and by the EnvZ-OmpR system converges at the porin promoters Batchelor E,2005.
The OmpR transcriptional factor cooperatively binds to the sites of the upstream regions from the ompFp promoter in a discontinuous galloping manner, as described by Yoshida T,2006
554 promoter regions from Escherichia coli were aligned in order to analyze their sequence similarities. Mitchell et al. (2003) Mitchell JE,2003 focused on conservation, patterns, similarities, and differences between promoters with or without an extended -10 5'-TG-3' element and other conserved elements. They experimentally showed that, for several naturally occurring extended -10 promoters, the 5'-TRTG-3' motif is an important determinant for promoter activity. Eleven promoters were selected for further experimental study. Of those, the seven most active (aroF > ompF > envA > purFp1 > purEF > purMN > gyrA) were investigated for the contribution of the extended -10 motif by changing the 5'-TG-3' motif. Promoters with poor matches to the -10 and -35 consensus hexamers are more dependent on the 5'-TG-3' motif, and this plays a similar role on different promoters. The dinucleotide at -17 and -16 in aroFp results in similar patterns of activity, suggesting that these bases play a similar role on different promoters Mitchell JE,2003.
Evidence: [CV(RS-EPT-CBR)]
[CV(TIM)]
[RS-EPT-CBR]
[TIM]
Reference(s): [2] Inokuchi K., et al., 1984
[3] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: gattgctctgGAAGGTATAAAAAAAACAGGACCAAAGTCCTGTTTTTTCGGCATTTAACAAAGAGgtgtgctatt
Reference(s): [4] Feng CQ., et al., 2019
[5] Lesnik EA., et al., 2001
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 CRP-cAMP activator ompFp 987134 987155 -52.5 tttgaaaccaAATCTTTATCTTTGTAGCACTTtcacggtagc nd [AIBSCS], [CV(GEA)], [GEA] [14]
proximal CRP-cAMP activator ompFp 987174 987195 -92.5 aagttccttaAATTTTACTTTTGGTTACATATtttttctttt nd [AIBSCS], [CV(GEA)], [GEA] [14]
remote CRP-cAMP activator ompFp 987203 987224 -121.5 gtctctatggAAATATGACGGTGTTCACAAAGttccttaaat nd [AIBSCS], [CV(GEA)], [GEA] [14]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CpxR-Phosphorylated1 repressor ompFp 987153 987169 -68.5 acatatttttTCTTTTTGAAACCAAATctttatcttt nd [AIBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [6], [7]
remote CpxR-Phosphorylated2 repressor ompFp 987178 987192 -93.0 ttccttaaatTTTACTTTTGGTTACatattttttc nd [AIBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [6], [7]
remote CpxR-Phosphorylated3 repressor ompFp 987458 987472 -373.0 cgatcatcctGTTACGGAATATTACattgcaacat nd [AIBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [6], [7]
remote CpxR-Phosphorylated4 repressor ompFp 987514 987530 -429.5 ttttctgtcaAGTTATCTGTTTGTTAAgtcaagcaat nd [AIBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [6], [7]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd EnvY activator ompFp nd nd nd nd nd [IMP] [25]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd Fur-Fe2+ activator ompFp nd nd nd nd nd [GEA] [14]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote IHF activator ompFp 987194 987206 -108.0 cggtgttcacAAAGTTCCTTAAAttttactttt nd [APIORCISFBSCS], [BCE] [13]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal IHF repressor ompFp 987148 987160 -62.0 ttctttttgaAACCAAATCTTTAtctttgtagc nd [APIORCISFBSCS], [BCE] [13]
remote IHF repressor ompFp 987262 987274 -176.0 aatataaggaAATCATATAAATAgattaaaatt nd [APIORCISFBSCS], [BCE] [13]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal OmpR-P activator ompFp 987133 987152 -50.5 gaaaccaaatCTTTATCTTTGTAGCACTTTcacggtagcg nd [AIBSCS], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM] [8], [10], [11], [12], [16], [17], [18], [19], [20], [21], [22], [23]
proximal OmpR-P activator ompFp 987153 987172 -70.5 gttacatattTTTTCTTTTTGAAACCAAATctttatcttt nd [APIORCISFBSCS], [BCE], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM] [9], [12], [13], [16], [17], [18], [19], [20], [21], [22], [23]
proximal OmpR-P3 activator ompFp 987173 987192 -90.5 ttccttaaatTTTACTTTTGGTTACATATTttttcttttt nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM] [12], [16], [17], [18], [19], [20], [21], [22]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal OmpR-P repressor ompFp 987133 987152 -50.5 gaaaccaaatCTTTATCTTTGTAGCACTTTcacggtagcg nd [AIBSCS], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM] [8], [10], [11], [12], [16], [17], [18], [19], [20], [21], [22], [23]
proximal OmpR-P repressor ompFp 987153 987172 -70.5 gttacatattTTTTCTTTTTGAAACCAAATctttatcttt nd [APIORCISFBSCS], [BCE], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM] [9], [12], [13], [16], [17], [18], [19], [20], [21], [22], [23]
remote OmpR-P3 repressor ompFp 987453 987472 -370.5 cgatcatcctGTTACGGAATATTACATTGCaacatttacg nd [BPP], [GEA] [8], [9], [10], [11], [12]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd PhoB-Phosphorylated activator ompFp nd nd nd nd nd [GEA] [24]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal RstA-Phosphorylated repressor ompFp 987176 987192 -92.0 ttccttaaatTTTACTTTTGGTTACATattttttctt nd [APIORCISFBSCS], [NAS] [15]
Note(s): 1Repression of ompF by CpxR could result from prevention of either OmpR or RNA polymerase binding Batchelor E,2005.
2Repression of ompF by CpxR could result from prevention of either OmpR or RNA polymerase binding Batchelor E,2005.
3Repression of ompF by CpxR could result from prevention of either OmpR or RNA polymerase binding Batchelor E,2005.
4Repression of ompF by CpxR could result from prevention of either OmpR or RNA polymerase binding Batchelor E,2005.3OmpR activates ompF at low osmolarity Forst SA,19893OmpR-P represses ompF at high osmolarity Forst SA,19891Repression of ompF by CpxR could result from prevention of either OmpR or RNA polymerase binding Batchelor E,2005.
2Repression of ompF by CpxR could result from prevention of either OmpR or RNA polymerase binding Batchelor E,2005.
3OmpR-P represses ompF at high osmolarity Forst SA,1989
7Repression of ompF by CpxR could result from prevention of either OmpR or RNA polymerase binding Batchelor E,2005.
10OmpR activates ompF at low osmolarity Forst SA,1989
13Repression of ompF by CpxR could result from prevention of either OmpR or RNA polymerase binding Batchelor E,2005.


Regulation by sRNA    
  Small RNA name (Regulator) Regulation type Mechanism Function Binding Sites Evidence Reference
LeftPos RightPos Sequence (RNA-strand)
  ipeX unknown post-transcriptional regulation repressor       [GEA]
[IMP]
[26]
  micF antisense translational regulation repressor 986973 986998 ATGAGGGTAATAAATAATGATGAAG
Notes: "The provided sequence is that of the RNA strand,i.e. 'U's are showed instead the 'T'"




Reference(s)    

 [1] Mizuno T., Chou MY., Inouye M., 1983, A comparative study on the genes for three porins of the Escherichia coli outer membrane. DNA sequence of the osmoregulated ompC gene., J Biol Chem 258(11):6932-40

 [2] Inokuchi K., Furukawa H., Nakamura K., Mizushima S., 1984, Characterization by deletion mutagenesis in vitro of the promoter region of ompF, a positively regulated gene of Escherichia coli., J Mol Biol 178(3):653-68

 [3] 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.

 [4] 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

 [5] 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

 [6] Batchelor E., Walthers D., Kenney LJ., Goulian M., 2005, The Escherichia coli CpxA-CpxR envelope stress response system regulates expression of the porins ompF and ompC., J Bacteriol 187(16):5723-31

 [7] Raivio TL., Leblanc SK., Price NL., 2013, The Escherichia coli Cpx envelope stress response regulates genes of diverse function that impact antibiotic resistance and membrane integrity., J Bacteriol 195(12):2755-67

 [8] Huang KJ., Schieberl JL., Igo MM., 1994, A distant upstream site involved in the negative regulation of the Escherichia coli ompF gene., J Bacteriol 176(5):1309-15

 [9] Oshima T., Aiba H., Masuda Y., Kanaya S., Sugiura M., Wanner BL., Mori H., Mizuno T., 2002, Transcriptome analysis of all two-component regulatory system mutants of Escherichia coli K-12., Mol Microbiol 46(1):281-91

 [10] Rampersaud A., Harlocker SL., Inouye M., 1994, The OmpR protein of Escherichia coli binds to sites in the ompF promoter region in a hierarchical manner determined by its degree of phosphorylation., J Biol Chem 269(17):12559-66

 [11] Slauch JM., Silhavy TJ., 1991, cis-acting ompF mutations that result in OmpR-dependent constitutive expression., J Bacteriol 173(13):4039-48

 [12] Yoshida T., Qin L., Egger LA., Inouye M., 2006, Transcription regulation of ompF and ompC by a single transcription factor, OmpR., J Biol Chem 281(25):17114-23

 [13] Ramani N., Huang L., Freundlich M., 1992, In vitro interactions of integration host factor with the ompF promoter-regulatory region of Escherichia coli., Mol Gen Genet 231(2):248-55

 [14] Zhang Z., Gosset G., Barabote R., Gonzalez CS., Cuevas WA., Saier MH., 2005, Functional interactions between the carbon and iron utilization regulators, Crp and Fur, in Escherichia coli., J Bacteriol 187(3):980-90

 [15] Ogasawara H., Hasegawa A., Kanda E., Miki T., Yamamoto K., Ishihama A., 2007, Genomic SELEX search for target promoters under the control of the PhoQP-RstBA signal relay cascade., J Bacteriol 189(13):4791-9

 [16] Forst SA., Delgado J., Inouye M., 1989, DNA-binding properties of the transcription activator (OmpR) for the upstream sequences of ompF in Escherichia coli are altered by envZ mutations and medium osmolarity., J Bacteriol 171(6):2949-55

 [17] Lan CY., Igo MM., 1998, Differential expression of the OmpF and OmpC porin proteins in Escherichia coli K-12 depends upon the level of active OmpR., J Bacteriol 180(1):171-4

 [18] Mattison K., Oropeza R., Byers N., Kenney LJ., 2002, A phosphorylation site mutant of OmpR reveals different binding conformations at ompF and ompC., J Mol Biol 315(4):497-511

 [19] Qin L., Yoshida T., Inouye M., 2001, The critical role of DNA in the equilibrium between OmpR and phosphorylated OmpR mediated by EnvZ in Escherichia coli., Proc Natl Acad Sci U S A 98(3):908-13

 [20] Rampersaud A., Norioka S., Inouye M., 1989, Characterization of OmpR binding sequences in the upstream region of the ompF promoter essential for transcriptional activation., J Biol Chem 264(31):18693-700

 [21] Sato M., Machida K., Arikado E., Saito H., Kakegawa T., Kobayashi H., 2000, Expression of outer membrane proteins in Escherichia coli growing at acid pH., Appl Environ Microbiol 66(3):943-7

 [22] Tsung K., Brissette RE., Inouye M., 1989, Identification of the DNA-binding domain of the OmpR protein required for transcriptional activation of the ompF and ompC genes of Escherichia coli by in vivo DNA footprinting., J Biol Chem 264(17):10104-9

 [23] Forst S., Kalve I., Durski W., 1995, Molecular analysis of OmpR binding sequences involved in the regulation of ompF in Escherichia coli., FEMS Microbiol Lett 131(2):147-51

 [24] Marzan LW., Hasan CM., Shimizu K., 2013, Effect of acidic condition on the metabolic regulation of Escherichia coli and its phoB mutant., Arch Microbiol 195(3):161-71

 [25] Lundrigan MD., Earhart CF., 1984, Gene envY of Escherichia coli K-12 affects thermoregulation of major porin expression., J Bacteriol 157(1):262-8

 [26] Castillo-Keller M., Vuong P., Misra R., 2006, Novel mechanism of Escherichia coli porin regulation., J Bacteriol 188(2):576-86


RegulonDB