RegulonDB RegulonDB 11.2: Operon Form
   

srkA-dsbA operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: srkA-dsbA
Synonym(s): rdoA-dsbA, yihE-dsbA
Gene(s): srkA, dsbA   Genome Browser M3D Gene expression COLOMBOS
Note(s): Under NlpE outer membrane lipoprotein overexpression, the transcription of the dsbA gene is increased Raivio TL,2013
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[EXP-IMP-POLAR-MUTATION] Polar mutation
Reference(s): [1] Belin P., et al., 1994
Promoter
Name: srkAp
+1: 4042391
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 24
Sequence: aagagtaaaagcttgtaagcggcgccaccaaaatcatcgtgaaatgatatccttcgtcatTcgtaatgttttccggatgat
                       -35                      -10         +1                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [1] Belin P., et al., 1994
[2] Huerta AM., et al., 2003
[3] Salgado H, et al., 2012
[4] Yamamoto K., et al., 2006
TF binding sites (TFBSs)
[CpxR,+] 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 CpxR-phosphorylated activator srkAp 4042341 4042342 -49.0 agagtaaaagCttgtaagcgg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [4], [5], [6]


Transcription unit       
Name: dsbA
Gene(s): dsbA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Belin P., et al., 1994
Promoter
Name: dsbAp
+1: 4043377
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 41
Sequence: ttactggctgcgacagacggcgacttttatagaacaggcaaaagttctacaagaacccccTttgcaattaacacctatgta
                          -35                   -10         +1                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [1] Belin P., et al., 1994
[2] Huerta AM., et al., 2003
[3] Salgado H, et al., 2012


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Translational
Strand: forward
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -13.4 4042378 4042417 gtgaaatgatATCCTTCGTCATTCGTAATGTTTTCCGGATGATGGGATGaataacagcg
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

 [COMP-HINF-POSITIONAL-IDENTIFICATION] Human inference of promoter position

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

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

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


Reference(s)    

 [1] Belin P., Boquet PL., 1994, The Escherichia coli dsbA gene is partly transcribed from the promoter of a weakly expressed upstream gene., Microbiology 140 ( Pt 12):3337-48

 [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] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

 [4] Yamamoto K., Ishihama A., 2006, Characterization of copper-inducible promoters regulated by CpxA/CpxR in Escherichia coli., Biosci Biotechnol Biochem 70(7):1688-95

 [5] Danese PN., Silhavy TJ., 1997, The sigma(E) and the Cpx signal transduction systems control the synthesis of periplasmic protein-folding enzymes in Escherichia coli., Genes Dev 11(9):1183-93

 [6] Pogliano J., Lynch AS., Belin D., Lin EC., Beckwith J., 1997, Regulation of Escherichia coli cell envelope proteins involved in protein folding and degradation by the Cpx two-component system., Genes Dev 11(9):1169-82

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