RegulonDB RegulonDB 10.8: Operon Form
   

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




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


Transcription unit          
Name: cspD
Gene(s): cspD   Genome Browser M3D Gene expression COLOMBOS
Note(s): cspD expression is induced during stationary phase and it is independent of σS Uppal S,2014 In addition, cspD is associated with biofilms and persister cell formation Uppal S,2014
CRP is activated via a class I-type mechanism that involves cspD expression Uppal S,2014 Based on mutant alleles, it was determined that the AR1 domain in CRP is critical for cspD activation, whereas the AR2 domain of CRP is not necessary Uppal S,2014
The mRNA produced by the cspD gene has been observed mainly in the poles of the cell 31540875.
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Yamanaka K., et al., 1997
Promoter
Name: cspDp
+1: 922676
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 86
Sequence: tgccccttgtcccctgtcaaatgcttgacggctcgccctaattctctaaattgtatttctAgagttggcgaggttttgaac
                         -35                   -10          +1                   
Note(s): The activity of this promoter appears to be decreased in the presence of σE. It is repressed during the first 5 minutes following σE induction and decreased from 5 to 10 minutes and from 10 to 20 minutes after induction of the σ factor Lacoux C,2020.
Evidence: [HIPP]
[TIM]
Reference(s): [1] Yamanaka K., et al., 1997
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 CRP-cAMP1 activator cspDp 922749 922770 -83.5 ttcctgtcaaTAGCGTTAACTGCTTCAAATTTttgattcata nd [AIBSCS], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM] [3]
remote CRP-cAMP2 activator cspDp 922778 922799 -112.5 tatcgttggcATCAGCGACATCTGTCACATTCctgtcaatag nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM] [3]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd H-NS activator cspDp nd nd nd nd nd [GEA] [1]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote MqsA1 repressor cspDp 922567 922585 101.5 gaagcatggaAAAGGGTACTGTTAAGTGGttcaacaatg nd [BPP], [GEA] [2]
remote MqsA2 repressor cspDp 922800 922818 -132.5 atgatagataACTATCATCTATCGTTGGCatcagcgaca nd [BPP], [GEA] [2]
Note(s): 1CRP site I is also called promoter-proximal, and it plays a major role in cspDp activation by CRP Uppal S,2014
2CRP site II site is also called distal-promoter, and it plays a minor role in cspDp activation by CRP Uppal S,20141Fraikin et al. Fraikin N,2019 showed that MqsA does not regulate the cspD promoter. The authors reported that the regulation observed in previous experiments could be nonspecific due to the disproportionate overexpression of the protein used in those earlier experiments.
2Fraikin et al. Fraikin N,2019 showed that MqsA does not regulate the cspD promoter. The authors reported that the regulation observed in previous experiments could be nonspecific due to the disproportionate overexpression of the protein used in those earlier experiments.1Fraikin et al. Fraikin N,2019 showed that MqsA does not regulate the cspD promoter. The authors reported that the regulation observed in previous experiments could be nonspecific due to the disproportionate overexpression of the protein used in those earlier experiments.
2CRP site II site is also called distal-promoter, and it plays a minor role in cspDp activation by CRP Uppal S,2014
3CRP site I is also called promoter-proximal, and it plays a major role in cspDp activation by CRP Uppal S,2014
4Fraikin et al. Fraikin N,2019 showed that MqsA does not regulate the cspD promoter. The authors reported that the regulation observed in previous experiments could be nonspecific due to the disproportionate overexpression of the protein used in those earlier experiments.
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  ppGpp activation cspDp   [GEA] [1]
Evidence: [GEA] Gene expression analysis
Reference(s): [1] Yamanaka K., et al., 1997





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