RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: ydeP
Gene(s): ydeP   Genome Browser M3D Gene expression COLOMBOS
Note(s): The transcription of ydeP appears to be increased under acidic growth conditions during the exponential phase in a RcsB-dependent manner, but not during stationary phase Johnson MD,2011
Masuda N,2003proposed a model of the regulatory network of the acid resistance genes, including evgA, ydeP, ydeO, yhiE, gadABC, and hdeAB, using a combination of microarray analysis and gene replacement techniques. With these assays, seven operons were identified as induced when EvgA is overexpressed and YdeO is absent; on the other hand, 12 operons were identified as induced when YdeO is overexpressed. To confirm these regulatory interactions, the EvgA consensus site was searched with the ALIGNACE program, and the 18-bp site found was tested by gel shift analysis with the upstream regions of the corresponding operons. As the result, just six operons are regulated by EvgA, among which the ydeP gene is included.
Based on results of gene expression analysis, EMSA, and a LacZ reporter assay, it was determined that the ydeP promotor is activated by five transcription factors: NarL, NarP, RcsB, UhpA, and UvrY Yoshida M,2015.
Reference(s): [1] Masuda N., et al., 2003
Promoter
Name: ydePp
+1: 1586664
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 178
Sequence: gcgcacaattgaagccagagtcttattttttatattgaaaaatatgttaatttaaacactAtgagagatgatgcttaactt
                                -35                  -10    +1                   
Note(s): The ydeP promoter is considered one of the group of multifactor promoters Aseev LV,2015
Evidence: [COMP-AINF]
[COMP-HINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Huerta AM., et al., 2003
[3] Itou J., et al., 2009
TF binding sites (TFBSs)
[EvgA,+] 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 EvgA-phosphorylated activator ydePp 1586730 1586747 -74.5 gaaggctattAGCCTACACCTGTAAGAAaatccgcgca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [1], [3]
[H-NS,-] 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
nd H-NS repressor ydePp nd nd nd nd nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [7]
[NagC,-] 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 NagC repressor ydePp 1586681 1586703 -28.0 aagccagagtCTTATTTTTTATATTGAAAAATAtgttaattta nd [COMP-AINF-SIMILAR-TO-CONSENSUS] nd nd
[NarL,+] 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
nd NarL-phosphorylated activator ydePp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [6]
[NarP,-] 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
nd NarP-phosphorylated repressor ydePp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [6]
[PhoP,-] 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
remote PhoP-phosphorylated repressor ydePp 1586622 1586640 34.5 ttaacttatcGTATTTAATCTATTGTTTAacgataatag nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [4]
[RcsB,+] 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
nd RcsB-phosphorylated activator ydePp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [5]
[UvrY,+] 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
nd UvrY-phosphorylated activator ydePp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [6]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

 [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis

 [COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences

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

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.


Reference(s)    

 [1] Masuda N., Church GM., 2003, Regulatory network of acid resistance genes in Escherichia coli., Mol Microbiol 48(3):699-712

 [2] 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

 [3] Itou J., Eguchi Y., Utsumi R., 2009, Molecular mechanism of transcriptional cascade initiated by the EvgS/EvgA system in Escherichia coli K-12., Biosci Biotechnol Biochem 73(4):870-8

 [4] Burton NA., Johnson MD., Antczak P., Robinson A., Lund PA., 2010, Novel aspects of the acid response network of E. coli K-12 are revealed by a study of transcriptional dynamics., J Mol Biol 401(5):726-42

 [5] Johnson MD., Burton NA., Gutierrez B., Painter K., Lund PA., 2011, RcsB Is Required for Inducible Acid Resistance in Escherichia coli and Acts at gadE-Dependent and -Independent Promoters., J Bacteriol 193(14):3653-6

 [6] Yoshida M., Ishihama A., Yamamoto K., 2015, Cross talk in promoter recognition between six NarL-family response regulators of Escherichia coli two-component system., Genes Cells 20(7):601-12

 [7] Krin E., Danchin A., Soutourina O., 2010, Decrypting the H-NS-dependent regulatory cascade of acid stress resistance in Escherichia coli., BMC Microbiol 10:273

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