RegulonDB RegulonDB 10.8: Operon Form
   

yqaE-kbp operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit       
Name: kbp
Gene(s): kbp   Genome Browser M3D Gene expression COLOMBOS
Note(s): Under NlpE outer membrane lipoprotein overexpression, the transcription of the ygaU gene is increased by CpxR Raivio TL,2013.
Evidence: [ICWHO] Inferred computationally without human oversight
Promoter
Name: kbpp4
+1: 2796814
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 28
Sequence: attaaacctgtgctcatccccgcggcgttaacgcgccgcgttcctctgctacactttctgAgtgtttccgttaacgaatga
                                                -10         +1                   
Note(s): Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 7.31. P-value: 1.340e-5
Evidence: [ICWHO]
Reference(s): [1] Huerta AM., et al., 2003


Transcription unit          
Name: yqaE-kbp
Gene(s): kbp, yqaE   Genome Browser M3D Gene expression COLOMBOS
Evidence: [PM] Polar mutation
Reference(s): [2] Bernal-Cabas M., et al., 2015
Promoter
Name: yqaEp
+1: 2797085
Distance from start of the gene: 57
Sequence: gcagcgtaaatgagagtaaaagcgtaagctgaaactggcaggctccgctaaaattactacGcttaagagataaaatctctt
Evidence: [TIM]
Reference(s): [3] De Lay N., et al., 2009
TF binding sites (TFBSs)
[CpxR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CpxR-Phosphorylated1 activator yqaEp 2797126 2797141 -48.0 gcctcagcagCGTAAATGAGAGTAAAagcgtaagct nd [AIBSCS], [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [2], [4], [5]
Note(s): 1The regulation of CpxR on the yqaE gene has been demonstrated via lacZ reporter gene expression experiments, quantitative PCR analysis of cDNA, and by the identification of a consensus DNA-binding site of CpxR in the regulatory region of yqaE Raivio TL,20131The regulation of CpxR on the yqaE gene has been demonstrated via lacZ reporter gene expression experiments, quantitative PCR analysis of cDNA, and by the identification of a consensus DNA-binding site of CpxR in the regulatory region of yqaE Raivio TL,2013


Transcription unit          
Name: yqaE
Gene(s): yqaE   Genome Browser M3D Gene expression COLOMBOS
Note(s): Under NlpE outer membrane lipoprotein overexpression, the transcription of the yqaE gene is increased by CpxR Raivio TL,2013
Evidence: [ICWHO] Inferred computationally without human oversight
[LTED] Length of transcript experimentally determined
Reference(s): [3] De Lay N., et al., 2009
Promoter
Name: yqaEp
+1: 2797085
Distance from start of the gene: 57
Sequence: gcagcgtaaatgagagtaaaagcgtaagctgaaactggcaggctccgctaaaattactacGcttaagagataaaatctctt
Evidence: [TIM]
Reference(s): [3] De Lay N., et al., 2009
TF binding sites (TFBSs)
[CpxR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CpxR-Phosphorylated1 activator yqaEp 2797126 2797141 -48.0 gcctcagcagCGTAAATGAGAGTAAAagcgtaagct nd [AIBSCS], [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [2], [4], [5]
Note(s): 1The regulation of CpxR on the yqaE gene has been demonstrated via lacZ reporter gene expression experiments, quantitative PCR analysis of cDNA, and by the identification of a consensus DNA-binding site of CpxR in the regulatory region of yqaE Raivio TL,20131The regulation of CpxR on the yqaE gene has been demonstrated via lacZ reporter gene expression experiments, quantitative PCR analysis of cDNA, and by the identification of a consensus DNA-binding site of CpxR in the regulatory region of yqaE Raivio TL,2013


Regulation by sRNA    
  Small RNA name (Regulator) Regulation type Mechanism Function Binding Sites Evidence Reference
LeftPos RightPos Sequence (RNA-strand)
  cyaR antisense post-transcriptional regulation repressor 2797013 2797032 ACATATGGGTTTCTGGAGA [IMP] [3]
Notes: "The provided sequence is that of the RNA strand,i.e. 'U's are showed instead the 'T'"


Evidence    

 [ICWHO] Inferred computationally without human oversight

 [TIM] Transcription initiation mapping

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [BPP] Binding of purified proteins

 [CV(GEA)] cross validation(GEA)

 [GEA] Gene expression analysis


Reference(s)    

 [1] 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

 [2] Bernal-Cabas M., Ayala JA., Raivio TL., 2015, The Cpx Envelope Stress Response Modifies Peptidoglycan Cross-Linking via the l,d-Transpeptidase LdtD and the Novel Protein YgaU., J Bacteriol 197(3):603-14

 [3] De Lay N., Gottesman S., 2009, The Crp-activated small noncoding regulatory RNA CyaR (RyeE) links nutritional status to group behavior., J Bacteriol 191(2):461-76

 [4] 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

 [5] Vogt SL., Evans AD., Guest RL., Raivio TL., 2014, The Cpx envelope stress response regulates and is regulated by small noncoding RNAs., J Bacteriol 196(24):4229-38

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