RegulonDB RegulonDB 10.9: 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 32571968.
Evidence: [ICWHO] 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: [IC]
[ICWHO]
Reference(s): [1] Dam S., et al., 2017


Transcription unit          
Name: ydbK-ompN
Gene(s): ompN, ydbK   Genome Browser M3D Gene expression COLOMBOS
Evidence: [ITCR] Inferred through co-regulation
Reference(s): [2] Fabrega A., et al., 2012
Promoter
Name: ydbKp
+1: 1440831
Distance from start of the gene: 47
Sequence: cacaaaagcgaaaatgcagaagaaagccatttgctaaaattgaaagattactactgggcgCgcagcaatttcgtgcgcccc
Evidence: [HTTIM]
Reference(s): [3] Raghavan R., et al., 2011
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 SoxS activator ydbKp 1440872 1440891 -50.5 gatgtgggggACACAAAAGCGAAAATGCAGAagaaagccat nd [APIORCISFBSCS], [BPP], [GEA], [SM] [4]
proximal SoxS activator ydbKp 1440876 1440895 -54.5 cgctgatgtgGGGGACACAAAAGCGAAAATGcagaagaaag nd [APIORCISFBSCS], [BPP], [GEA], [SM] [4]


Transcription unit          
Name: ydbK
Gene(s): ydbK   Genome Browser M3D Gene expression COLOMBOS
Evidence: [AISGDTU] 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: [HTTIM]
Reference(s): [3] Raghavan R., et al., 2011
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 SoxS activator ydbKp 1440872 1440891 -50.5 gatgtgggggACACAAAAGCGAAAATGCAGAagaaagccat nd [APIORCISFBSCS], [BPP], [GEA], [SM] [4]
proximal SoxS activator ydbKp 1440876 1440895 -54.5 cgctgatgtgGGGGACACAAAAGCGAAAATGcagaagaaag nd [APIORCISFBSCS], [BPP], [GEA], [SM] [4]


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: [ITCR] Inferred through co-regulation
Reference(s): [2] 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                   
Note(s): Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.7. P-value: 7.411e-5
Evidence: [ICWHO]
[IHBCE]
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
Evidence: [ICA] Inferred by computational analysis
Reference(s): [7] Merino E, et al., 2005
  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"





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