RegulonDB RegulonDB 11.2: Operon Form
   

ydbK-ompN operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit       
Name: ompN
Gene(s): ompN   Genome Browser M3D Gene expression COLOMBOS
Note(s): Expression levels of both micC and ompN are increased in the presence of -lactam antibiotics. On the other hand, under conditions when cells were depleted of σE upon overexpression of its cognate anti-sigma RseA, the activities of both micC and the ompN-lacZ fusion were affected. However, the σE core promoter motif was not found, which suggests an indirect effect Dam S,2017 Finally, based on gene expression analysis, it was shown that H-NS could be regulating the expression of micC and ompN Dam S,2017
MicC sRNA could be acting together with σE to control OmpC/N levels in response to -lactam antibiotics Dam S,2017
The transcription of the ompN gene is induced during the first 24 h after the induction of nitrogen starvation Switzer A, Burchell L, McQuail J, Wigneshweraraj S,2020.
Evidence: [COMP-AINF] Inferred computationally without human oversight
Promoter
Name: ompNp
+1: 1437013
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 120
Sequence: tatgtattatcttcgatacattcaccagacttattatcatttcagaggaattatttgattAaggttttacttaaggcgtaa
                          -35                         -10   +1                   
Evidence: [COMP-AINF]
[IC]
Reference(s): [1] Dam S., et al., 2017


Transcription unit          
Name: ydbK
Gene(s): ydbK   Genome Browser M3D Gene expression COLOMBOS
Evidence: [COMP-AINF-SINGLE-DIRECTON] Automated inference that a single-gene directon is a transcription unit
Promoter
Name: ydbKp
+1: 1440831
Distance from start of the gene: 47
Sequence: cacaaaagcgaaaatgcagaagaaagccatttgctaaaattgaaagattactactgggcgCgcagcaatttcgtgcgcccc
Evidence: [EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP]
Reference(s): [2] Raghavan R., et al., 2011
TF binding sites (TFBSs)
[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 ydbKp 1440872 1440891 -50.5 atgtgggggaCACAAAAGCGAAAATGCAGAagaaagccat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [3]
proximal SoxS activator ydbKp 1440876 1440895 -54.5 gctgatgtggGGGACACAAAAGCGAAAATGcagaagaaag nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [3]


Transcription unit          
Name: ydbK-ompN
Gene(s): ompN, ydbK   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s): [4] Fabrega A., et al., 2012
Promoter
Name: ydbKp
+1: 1440831
Distance from start of the gene: 47
Sequence: cacaaaagcgaaaatgcagaagaaagccatttgctaaaattgaaagattactactgggcgCgcagcaatttcgtgcgcccc
Evidence: [EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP]
Reference(s): [2] Raghavan R., et al., 2011
TF binding sites (TFBSs)
[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 ydbKp 1440872 1440891 -50.5 atgtgggggaCACAAAAGCGAAAATGCAGAagaaagccat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [3]
proximal SoxS activator ydbKp 1440876 1440895 -54.5 gctgatgtggGGGACACAAAAGCGAAAATGcagaagaaag nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [3]


Transcription unit       
Name: ydbK-ompN
Gene(s): ompN, ydbK   Genome Browser M3D Gene expression COLOMBOS
Note(s): ydbK-ompN operon can be indirectly activated by the SoxS Fabrega A,2012 This effect was determined in the PS5 and NorE5 uropathogenic Escherichia coli clinical strains Fabrega A,2012
Evidence: [EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s): [4] Fabrega A., et al., 2012
Promoter
Name: ydbKp4
+1: 1440846
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 62
Sequence: cgctgatgtgggggacacaaaagcgaaaatgcagaagaaagccatttgctaaaattgaaaGattactactgggcgcgcagc
                                                       -10  +1                   
Evidence: [COMP-AINF]
[COMP-HINF]
[EXP-IDA]
Reference(s): [5] Huerta AM., et al., 2003
[6] Peano C., et al., 2015


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -15.1 1440956 1440998 gcagcacagaGGGCGGCGTCGAGAGCTGTCCTGCGCGTTGCCCCGCATTTTTacttttttat
  anti-terminator -13.85 1440988 1441029 tcaagccaaaCGACACCGCCATAAATAATAGGCAGCACAGAGGGCGGCGTCgagagctgtc
  anti-anti-terminator -8.3 1441068 1441085 aataaagcggCACACCCTACCCAAAACgctgctcgca
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"


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [IC] Inferred by curator

 [EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP] High-throughput 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-CHIP-EXO] high throughput ChIP-exo evidence

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

 [EXP-IMP-SITE-MUTATION] Site mutation

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

 [EXP-IDA] Inferred from direct assay


Reference(s)    

 [1] Dam S., Pages JM., Masi M., 2017, Dual Regulation of the Small RNA MicC and the Quiescent Porin OmpN in Response to Antibiotic Stress in Escherichia coli., Antibiotics (Basel) 6(4)

 [2] Raghavan R., Sage A., Ochman H., 2011, Genome-wide identification of transcription start sites yields a novel thermosensing RNA and new cyclic AMP receptor protein-regulated genes in Escherichia coli., J Bacteriol 193(11):2871-4

 [3] Nakayama T., Yonekura S., Yonei S., Zhang-Akiyama QM., 2013, Escherichia coli pyruvate:flavodoxin oxidoreductase, YdbK - regulation of expression and biological roles in protection against oxidative stress., Genes Genet Syst 88(3):175-88

 [4] Fabrega A., Rosner JL., Martin RG., Sole M., Vila J., 2012, SoxS-dependent coregulation of ompN and ydbK in a multidrug-resistant Escherichia coli strain., FEMS Microbiol Lett 332(1):61-7

 [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] Peano C., Wolf J., Demol J., Rossi E., Petiti L., De Bellis G., Geiselmann J., Egli T., Lacour S., Landini P., 2015, Characterization of the Escherichia coli σ(S) core regulon by Chromatin Immunoprecipitation-sequencing (ChIP-seq) analysis., Sci Rep 5:10469

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