RegulonDB RegulonDB 10.8: Operon Form
   

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




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


Transcription unit       
Name: ompA
Gene(s): ompA   Genome Browser M3D Gene expression COLOMBOS
Note(s): FNR represses ompA gene expression under anaerobiosis, but it is still unknown which of the two promoters (ompAp1 or ompAp2) is affected, or whether this regulation is direct or indirect Salmon K,2003.
It was proved in an experiment with increasing concentrations of the antibiotic tetracycline that the ompA gene expression is induced in low concentrations (1.5 and 4 mg/L), but not in high ones (10 mg/L); this suggests that the product of this gene plays a role under this condition 17426813
Evidence: [BTEI] Boundaries of transcription experimentally identified
[LTED] Length of transcript experimentally determined
Reference(s): [1] Beck E., et al., 1980
[2] Movva NR., et al., 1980
Promoter
Name: ompAp2
+1: 1020187
Distance from start of the gene: 134
Sequence: tttcatatgcctgacggagttcacacttgtaagttttcaactacgttgtagactttacatCgccaggggtgctcggcataa
Note(s): The TSS in ompAp2 identified by Liu et al. (2018) using Capping-RACE differs by 1 bp from that identified by Cole et al. (1982) Liu F,2018
Evidence: [CV(RS-EPT-CBR)]
[CV(TIM)]
[HTIM]
[RS-EPT-CBR]
[TIM]
Reference(s): [3] Cole ST., et al., 1982
[4] Liu F., et al., 2018
[5] Salgado H, et al., 2012


Transcription unit          
Name: ompA
Synonym(s): OP00064
Gene(s): ompA   Genome Browser M3D Gene expression COLOMBOS
Note(s): FNR represses ompA gene expression under anaerobiosis, but it is still unknown which of the two promoters (ompAp1 or ompAp2) is affected, or whether this regulation is direct or indirect Salmon K,2003.
It was proved in an experiment with increasing concentrations of the antibiotic tetracycline that the ompA gene expression is induced in low concentrations (1.5 and 4 mg/L), but not in high ones (10 mg/L); this suggests that the product of this gene plays a role under this condition 17426813
Evidence: [BTEI] Boundaries of transcription experimentally identified
[LTED] Length of transcript experimentally determined
Reference(s): [1] Beck E., et al., 1980
[2] Movva NR., et al., 1980
Promoter
Name: ompAp1
+1: 1020191
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 138
Sequence: tttttttcatatgcctgacggagttcacacttgtaagttttcaactacgttgtagactttAcatcgccaggggtgctcggc
                               -35                   -10    +1                   
Evidence: [TIM]
Reference(s): [3] Cole ST., et al., 1982
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 ompAp1 1020220 1020241 -39.5 tttttttcatATGCCTGACGGAGTTCACACTTgtaagttttc nd [APIORCISFBSCS], [CV(GEA)], [GEA] [6], [7]


Regulation by sRNA    
  Small RNA name (Regulator) Regulation type Mechanism Function Binding Sites Evidence Reference
LeftPos RightPos Sequence (RNA-strand)
  micA antisense translational regulation repressor 1020060 1020075 GGATGATAACGAGGC [GEA]
[HIFS]
[IMP]
[IPI]
[8]
  rseX antisense post-transcriptional regulation repressor 1020061 1020075 GGATGATAACGAGG [HIFS]
[IE]
[IMP]
[IPI]
[9]
Notes: "The provided sequence is that of the RNA strand,i.e. 'U's are showed instead the 'T'"


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -11.5 1020076 1020112 aaggatttaaCCGTGTTATCTCGTTGGAGATATTCATGGCGTATTTtggatgataa
  anti-terminator -6.3 1020098 1020138 gttaatattgAGCAGATCCCCCGGTGAAGGATTTAACCGTGTTATCTCGTtggagatatt
  anti-anti-terminator -5.6 1020123 1020158 aagccgaagaTATCGGTAGAGTTAATATTGAGCAGATCCCCCGGTgaaggattta
Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos"




Reference(s)    

 [1] Beck E., Bremer E., 1980, Nucleotide sequence of the gene ompA coding the outer membrane protein II of Escherichia coli K-12., Nucleic Acids Res 8(13):3011-27

 [2] Movva NR., Nakamura K., Inouye M., 1980, Regulatory region of the gene for the ompA protein, a major outer membrane protein of Escherichia coli., Proc Natl Acad Sci U S A 77(7):3845-9

 [3] Cole ST., Bremer E., Hindennach I., Henning U., 1982, Characterisation of the promoters for the ompA gene which encodes a major outer membrane protein of Escherichia coli., Mol Gen Genet 188(3):472-9

 [4] Liu F., Zheng K., Chen HC., Liu ZF., 2018, Capping-RACE: a simple, accurate, and sensitive 5' RACE method for use in prokaryotes., Nucleic Acids Res 46(21):e129

 [5] 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.

 [6] Gibert I., Barbe J., 1990, Cyclic AMP stimulates transcription of the structural gene of the outer-membrane protein OmpA of Escherichia coli., FEMS Microbiol Lett 56(3):307-11

 [7] Movva RN., Green P., Nakamura K., Inouye M., 1981, Interaction of cAMP receptor protein with the ompA gene, a gene for a major outer membrane protein of Escherichia coli., FEBS Lett 128(2):186-90

 [8] Udekwu KI., Darfeuille F., Vogel J., Reimegard J., Holmqvist E., Wagner EG., 2005, Hfq-dependent regulation of OmpA synthesis is mediated by an antisense RNA., Genes Dev 19(19):2355-66

 [9] Douchin V., Bohn C., Bouloc P., 2006, Down-regulation of porins by a small RNA bypasses the essentiality of the regulated intramembrane proteolysis protease RseP in Escherichia coli., J Biol Chem 281(18):12253-9


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