RegulonDB RegulonDB 11.2: Operon Form
   

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




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


Transcription unit          
Name: tppB
Synonym(s): ydgR
Gene(s): dtpA   Genome Browser M3D Gene expression COLOMBOS
Note(s): Analysis of gene expression has proved that under NlpE lipoprotein overexpression, the presence of the protein CpxR causes decreased transcription of the tppB gene; however, no DNA sequence related to the consensus DNA-binding site of CpxR has been identified in the regulatory region of the gene. Therefore, the effect of CpxR on tppB is probably indirect Raivio TL,2013
Promoter
Name: tppBp
+1: 1712671
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 98
Sequence: tatatgtaacagattattacaaaggacttgtctgaaagtgcaagatagtgaacattacctGccgtttcccctcccactata
                 -35                        -10             +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Goh EB., et al., 2004
[2] Huerta AM., et al., 2003
TF binding sites (TFBSs)
[GadX,-] 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 GadX repressor tppBp 1712510 1712529 -151.0 cgttaagccaTCACCCCCCTCTCAGTGCAGtgaaaaaatc nd [EXP-IEP-RNA-SEQ], [COMP-HINF], [EXP-CHIP-EXO-MANUAL] S [3]
[OmpR,+] 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 OmpR-phosphorylated activator tppBp 1712616 1712635 -45.5 tcagttatatGTAACAGATTATTACAAAGGacttgtctga nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-CHIP-SEQ], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [1]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Translational
Strand: forward
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -6.2 1712730 1712752 cgcgagaaagCACCCCCGTTAATATGGGATGTaaaaaaagag
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

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

 [EXP-IEP-RNA-SEQ] high throughput RNA-seq evidence

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

 [EXP-CHIP-EXO-MANUAL] ChIP-exo evidence used in manual assertion

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

 [EXP-CHIP-SEQ] high throughput ChIP-seq evidence

 [EXP-DAP-SEQ] high throughput DNA Affinity Purification (DAP) Sequencing

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


Reference(s)    

 [1] Goh EB., Siino DF., Igo MM., 2004, The Escherichia coli tppB (ydgR) gene represents a new class of OmpR-regulated genes., J Bacteriol 186(12):4019-24

 [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] Seo SW., Kim D., O'Brien EJ., Szubin R., Palsson BO., 2015, Decoding genome-wide GadEWX-transcriptional regulatory networks reveals multifaceted cellular responses to acid stress in Escherichia coli., Nat Commun 6:7970

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